Transposable elements in rice and methods of use

ABSTRACT

Disclosed are isolated transposable elements, or isolated DNA sequences which encode a transposase protein or a portion of a transposase protein. The isolated transposable elements or the isolated DNA sequences are members of the mPing/Pong family of transposable elements. The invention also relates to a purified transposase protein, or peptide fragments thereof, encoded by such DNA sequences. Such transposable elements are useful in applications such as the stable introduction of a DNA sequence of interest into a eukaryotic cell. The sequence information disclosed herein is useful in the design of oligonucleotide primers which are useful for the isolation of related members of the mPing/Pong family of transposable elements, or for the detection of transpositions of the transposable elements.

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] The present invention claims the priority benefit of U.S. Provisional Patent Application Serial No. 60/377,409 filed May 1, 2002, the entire contents of which are hereby incorporated by reference.

ACKNOWLEDGMENT OF FEDERAL RESEARCH SUPPORT

[0002] This invention was made, at least in part, with funding from the National Science Foundation (DBI 0077709) to SRW. Accordingly, the United States Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

[0003] 1. Field of the Invention

[0004] This invention relates generally to nucleic acid sequences encoding members of the mPing/Pong family of transposable elements. In addition, this invention relates to nucleic acid sequences encoding polypeptides that function as transposases, or polypeptides that interact with transposases to modulate the transposition of members of the mPing/Pong genus of transposable elements.

[0005] 2. Background Art

[0006] Rice is the most important crop for human nutrition in the world. At 430 Mb, rice also has the smallest genome among the agriculturally important cereals, including the genomes of maize, sorghum, barley and wheat (Arumuganathan & Earle, 1991 Plant Mol. Biol., 9: 208-218). For these reasons rice is the focus of several genome sequencing projects in both the public and private sectors (Burr, 2002 Plant Cell, 14: 521-523; Goff, et al., 2002 Science, 296: 92-100; Yu, et al., 2002 Science, 296: 79-92). Computer-assisted analyses of rice genomic sequence indicate that despite its small size, over 40% of the genome is repetitive DNA; most of this is related to transposable elements (Goff, et al., 2002 Science, 296: 92-100; Yu, et al., 2002 Science, 296: 79-92). Although the largest component of transposable elements in the rice genome is class 1 LTR retrotransposons (14%), the largest group with over 100,000 elements divided into hundreds of families is miniature inverted-repeat transposable elements (MITEs), comprising about 6% of the genome (Tarchini et al., 2000 Plant Cell, 12: 381-391; Jiang & Wessler, 2001 Plant Cell, 13: 2553-2564). MITEs are the predominant transposable element associated with the noncoding regions of the genes of flowering plants, especially the grasses and have been found in several animal genomes including nematodes, mosquitoes, fish, and humans (reviewed in Feschotte et al., 2002 Nat. Rev. Genet., 3: 329-341).

[0007] MITEs are structurally reminiscent of nonautonomous DNA (class 2) elements with their small size (less than 600 bp) and short (10 to 30 bp) terminal inverted repeat (TIR). However, their high copy number (up to 10,000 copies/family) and target-site preference for TA or TAA distinguish them from most previously described nonautonomous DNA elements (Feschotte et al., 2002 Nat. Rev. Genet., 3: 329-341). Nonautonomous elements, which make up a significant fraction of eukaryotic genomes, have been classified into families based on the transposase responsible for their mobility. Classifying MITEs in this way has been problematic because no actively transposing MITE had been reported in any organism. Instead, based on the similarity of their TIRs and their target site duplication (TSD), most of the tens of thousands of plant MITEs have been classified into two superfamilies: Tourist-like MITEs and Stowaway-like MITEs (Jiang & Wessler, 2001 Plant Cell, 13: 2553-2564; Turcotte et al., 2001 Plant J., 25: 169-179; Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285). Recently, evidence has accumulated linking Tourist and Stowaway MITEs with two superfamilies of transposases, PIF/IS5 and Tcl/mariner, respectively (Turcotte et al., 2001 Plant J., 25: 169-179; Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285; Zhang, et al., Proc. Natl. Acad. Sci. USA, 98: 12572-12577).

[0008] Activity has not been demonstrated for any of the hundreds of MITE families previously identified in the rice genome, however three families of LTR retrotransposons, Tos10, Tos17, and Tos19, have been shown to transpose in both japonica (Nipponbare) and indica (C5924) cell culture (Hirochika, et al., 1996 Proc. Natl. Acad. Sci. USA, 93: 7783-7788). Similarly, no activity has been associated with the hundreds of MITE families from either plants or animals. Most MITE families are characterized by high copy number (hundreds to thousands per haploid genome) and intra-family sequence identity that is rarely over 95% (Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285). Since newly amplified elements are usually identical, these families have most likely been inactive for hundreds of thousands or even millions of years. In addition, to date, only a single active DNA transposon, Tol2, has been isolated from a vertebrate (Kawakami, et al., 2000 Proc. Natl. Acad. Sci. USA, 97: 11403-8), and no active DNA transposons have been isolated from mammals.

[0009] Because no activity has been demonstrated for any of the known MITE families in either plants or animals, there is a need in the art to identify MITEs and related transposable elements that are actively transposing.

SUMMARY OF THE INVENTION

[0010] It is an object of the present invention to overcome, or at least alleviate, one or more of the difficulties or deficiencies associated with the prior art. In that regard, the present invention fulfills in part the need to identify new, unique transposable elements capable of actively transposing, at least in plants. The present invention describes a novel genus of Pong-like Transposase Polypeptides (PTPs) and Pong-like Transposable Element (PTE) nucleic acids. The novel genus is the mPing/Pong family of DNA transposable elements, and the Pong family of transposases. Preferably, the mPing/Pong family of DNA transposable elements is capable of actively transposing, and comprises two terminal inverted repeats.

[0011] The present invention includes an isolated cell comprising a PTP-encoding nucleic acid, wherein expression of the nucleic acid sequence in the cell results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the cell. The invention further comprises an isolated cell comprising a nucleic acid sequence comprising a transposable element of the mPing/Pong family of transposable elements.

[0012] The invention provides in some embodiments that the PTP-encoding and PTE nucleic acid are those that are found in members of the genus Brassica, or Oryza. In another preferred embodiment, the nucleic acid and polypeptide are from a Brassica oleracea plant or an Oryza sativa plant.

[0013] The invention further provides a seed produced by a transgenic plant transformed by a PTP-encoding or PTE containing nucleic acid, wherein the plant is true breeding for increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the plant. The invention further provides a seed produced by a transgenic plant expressing a PTP, wherein the plant is true breeding for increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the plant.

[0014] The invention further provides an agricultural product produced by any of the below-described transgenic plants, plant parts or seeds. The invention further provides an isolated PTP as described below. The invention further provides an isolated PTP-encoding nucleic acid, wherein the PTP-encoding nucleic acid codes for a PTP as described below.

[0015] The invention further provides an isolated recombinant expression vector comprising a PTP-encoding nucleic acid as described below, wherein expression of PTP from the vector in a host cell results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the host cell. The invention further provides an isolated recombinant expression vector comprising a PTE nucleic acid as described below, wherein expression of PTP from the vector in a host cell results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the host cell. The invention further provides a host cell containing at least one of the vectors described above and a plant containing the host cell.

[0016] The invention further provides a method of producing a transgenic plant with a PTP-encoding nucleic acid or a PTE nucleic acid, wherein expression of the nucleic acid in the plant results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the plant comprising: (a) transforming a plant cell with an expression vector comprising a PTP-encoding nucleic acid or a PTE nucleic acid, and (b) generating from the plant cell a transgenic plant. In preferred embodiments, the PTP, PTP coding nucleic acid, and PTE nucleic acid are as described below.

[0017] The present invention further provides a method of identifying a novel PTP, comprising (a) raising a specific antibody that binds to a PTP, or fragment thereof, as described below; (b) screening putative PTP material with the antibody, wherein specific binding of the antibody to the material indicates the presence of a potentially novel PTP; and (c) identifying from the bound material a novel PTP in comparison to known PTP. Alternatively, hybridization with nucleic acid probes as described below can be used to identify novel PTP-encoding and PTE-containing nucleic acids.

[0018] The present invention also provides methods of identifying an active transposable element in a sample, comprising combining an active transposable element with a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to the transposable element and detecting hybridization, thereby identifying the transposable element. In a preferred embodiment, the active transposable element is a member of the mPing/Pong family of transposable elements.

[0019] The present invention also provides methods of screening a cell for a transposition of a transposable element, wherein the transposable element is actively transposing, comprising the steps of: a) providing a cell comprising a transposable element, b) inducing a transposition of the transposable element by a transposase comprising a nucleic acid sequence and c) comparing the phenotype of the cell containing the transposition of the transposable element to a wild-type cell not containing a transposition of the transposable element to thereby screen for a cell containing the transposition. In a preferred embodiment, the transposable element is a member of the mPing/Pong family of transposable elements.

BRIEF DESCRIPTION OF THE DRAWINGS

[0020]FIG. 1 shows a comparison of mPing, Ping and Pong elements. Black triangles represent TIRs and black boxes represent putative N2, N3 and C1 catalytic domains. The nucleotide sequences of the TIRs/TSDs and amino acid sequences of the catalytic domains of the rice Pong, the maize PIF (Zhang, et al., 2001 Proc. Natl. Acad. Sci. USA, 98: 12572-12577) and the bacterial IS1031c and IS112 elements are shown. The thick vertical black line in mPing stands for internal sequences that differ among the four subtypes derived from Ping. An alignment of this region is at the top. The arrowhead indicates the breakpoint in Ping where 4923 bp of its internal sequence is not shown in alignment.

[0021]FIG. 2 shows the Accession number of mPing-containing rice sequences in GenBank. The chromosome number, the Accession number, the position, the orientation and the strain of rice are all indicated.

[0022]FIG. 3 shows an autoradiograph of transposon display gels of mPing, ID-1, SZ-2, and Pong amplicons with rice genomic DNAs isolated before and after cell culture. The same genomic DNAs (digested and ligated with adapters) were used for each set of primers: 1, Nipponbare; 2, calli of Nipponbare; 3, C5924; 4, Oc cell lines derived from C5924 (Baba, et al., 1986 Plant Cell Physiol., 27: 463-471). The migration of DNA markers is on the left in base pairs.

[0023]FIG. 4 shows the Accession number of Ping-containing rice sequences in GenBank. The chromosome number, the Accession number, the position, the orientation and the strain of rice are all indicated.

[0024]FIG. 5 shows the Accession number of Pong-containing rice sequences in GenBank. The chromosome number, the Accession number, the position, the orientation and the strain of rice are all indicated.

[0025]FIG. 6 shows the position of the Pong-containing rice sequences in 93-11 (indica). The contig number, the position, and the orientation of the sequences are all indicated.

[0026]FIG. 7 shows a list of organisms that contain Pif-like transposes. Pif-like transposes are present in plants (monocots, dicots, and algae), animals (vertebrates and invertebrates), and fungus.

[0027]FIG. 8 shows a list of the new insertion sites of mPing and Pong in the C5924 cell line, where the insertion sites were determined using transposon display.

[0028]FIGS. 9A and B show autoradiographs of transposon display gels of mPing (A) and Pong (B). The genomic DNA in each respective lane is: 1, Nipponbare; 2, Gihobyeo; 3, JX 17; 4, Koshikari; 5, Calrose; 6, Early Wataribune; 7, Shinriki; 8, Azucena; 9, Lemont; 10, Jefferson; 11, Moroberekan; 12, Rexoro; 13, Wab56-104; 14, Carolina Gold; 15, Kaybonnet; 16, C5924; 17, IR64; 18, Kasalath; 19, GuangLuAi4; 20, 93-11; 21, Tequing; 22, IR36; 23, Bs125. The migration of DNA markers is on the left in base pairs.

[0029]FIGS. 10A and B show the phylogeny of Pong-like transposable elements in B. oleracea and A. thaliana. (A) shows a neighbor-joining tree generated from a multiple alignment of the catalytic domains of 139 Pong-like transposases from B. oleracea and 28 from A. thaliana, rooted with the catalytic domain of Pong transposase (ORF2, SEQ ID NO:13). (B) shows a neighbor-joining tree generated from a multiple alignment of 170 Pong-like ORF1s from B. oleracea and 6 from A. thaliana, rooted with the ORF1 of the rice Pong element (ORF2, SEQ ID NO:12). Elements were named after the species initials, followed by GenBank accession numbers. Bootstrap values were calculated from 1,000 replicates.

DETAILED DESCRIPTION OF THE INVENTION

[0030] The present invention provides in certain embodiments an isolated transposable element comprising two terminal inverted repeat nucleic acid sequences, wherein the transposable element is actively transposing. The transposable element of the present invention can be transposed and inserted into various sites on chromosomes. By means of this ability, the transposable element of the present invention can be used as effective means for a variety of genetic techniques. Examples of these practical applications include, but are not limited to, creation of insertion mutant strains, gene mapping, promoter searching, insertion of genetic information, disruption of a specific gene or genes and the like.

[0031] Unless otherwise noted, the terms used herein are to be understood according to conventional usage by those of ordinary skill in the relevant art. In addition to the definitions of terms provided below, definitions of common terms in molecular biology may also be found in Rieger et al., 1991 Glossary of genetics: classical and molecular, 5th Ed., Berlin: Springer-Verlag; and in Current Protocols in Molecular Biology, F. M. Ausubel et al., Eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1998 Supplement). It is to be understood that as used in the specification and in the claims, “a” or “an” can mean one or more, depending upon the context in which it is used. Thus, for example, reference to “a cell” can mean that at least one cell can be utilized.

[0032] The present invention may be understood more readily by reference to the following detailed description of the preferred embodiments of the invention and the Examples included herein. However, before the present compounds, compositions, and methods are disclosed and described, it is to be understood that this invention is not limited to specific nucleic acids, specific polypeptides, specific cell types, specific host cells, specific conditions, or specific methods, etc., as such may, of course, vary, and the numerous modifications and variations therein will be apparent to those skilled in the art. It is also to be understood that the terminology used herein is for the purpose of describing specific embodiments only and is not intended to be limiting.

[0033] The present invention describes a novel genus of Pong-like Transposase Polypeptides (PTPs) and Pong-like Transposable Element (PTE) nucleic acids. The novel family is the mPing/Pong family of DNA transposable elements, and the Pong family of transposases. Preferably, the mPing/Pong family of DNA transposable elements is capable of actively transposing, and comprises two terminal inverted repeats.

[0034] The term “transposable element,” as used herein, refers to a DNA sequence whose excision from or insertion into genomic DNA is catalyzed by a functional transposase protein encoded by a non-defective member of the family of transposable elements. A member of the Pong family which encodes a functional transposase and possesses other necessary cis-acting elements (e.g., terminal inverted repeats) falls within this definition. In addition, a transposable element which encodes a defective transposase (e.g., Ping) falls within this definition. Furthermore, a transposable element that does not encode a transposase, but possesses the necessary cis-acting elements (i.e. mPing) falls within this definition. As discussed in greater detail below, such transposable elements that do not encode a functional transposase can be used in conjunction with a helper element (i.e., a member of the mPing/Pong family which encodes a functional transposase) to introduce a DNA sequence of interest into a eukaryotic cell.

[0035] The invention also relates to an isolated DNA sequence encoding a functional transposase protein, or a portion of a transposase protein, encoded by a member of the mPing/Pong family. Such a DNA sequence need not retain the ability to transpose in the presence of the encoded transposase protein. A sequence encoding a functional transposase protein can be used to prepare an expression construct which can be used to produce the transposase protein by recombinant DNA methodology. Such a recombinant protein can be over-produced in a eukaryotic (e.g., yeast) or prokaryotic (e.g., E. coli) host cell, and subsequently purified by conventional methods.

[0036] The active transposase can be used in a variety of ways. For example, as discussed below, the transposase protein or a transposase-producing vector can be co-introduced into a eukaryotic cell with a modified transposon carrying a DNA sequence of interest to catalyze the insertion of the modified transposon into the genomic DNA of the eukaryotic cell. This is an alternative to the co-introduction of a helper construct in eukaryotic cells which do not constitutively produce the mPing/Pong transposase.

[0037] In addition, the transposase, or portions thereof, can be used to produce antibodies (monoclonal and polyclonal) reactive with the transposase protein. Methods for the production of monoclonal and polyclonal antibodies are well-known in the art once a purified antigen is available.

[0038] As used herein, the terms “active transposable element” and “actively transposing” refer to the capacity of the DNA transposable element to change location within the genome of an organism. Preferably, the change of location occurs at a rate higher than 1 translocation per 1000 years, and more preferably at a rate higher than 1 translocation per 100 years. The transposable element can be induced to change location through cultivating a cell containing a mPing/Pong transposable element and a nucleic acid encoding a functional mPing/Pong transposase in cell culture. Other methods of inducing the translocation of a mPing/Pong transposable element are contemplated.

[0039] The present invention describes for the first time that the rice mPing, and Pong elements, and the Brassica oleracea Pong elements are actively transposing transposable elements of the PTE superfamily. Table 1 provides a quick reference for the identification of the nucleic acid sequences and amino acid sequences provided herein. TABLE 1 Identification Sequence Identification Numbers Nucleotide sequences SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, of mPing in rice and SEQ ID NO: 4 Nucleotide sequence SEQ ID NO: 5 of Ping in rice Amino acid sequence SEQ ID NO: 6 of ORF1 of Ping in rice Amino acid sequence SEQ ID NO:7 of ORF2 of Ping in rice Nucleotide sequences SEQ ID NO: 8; SEQ ID NO: 9; SEQ ID NO: 10; of Pong in rice SEQ ID NO: 11; SEQ ID NO: 14; SEQ ID NO: 17; SEQ ID NO: 20; SEQ ID NO: 23; SEQ ID NO: 26; SEQ ID NO: 29; SEQ ID NO: 32; SEQ ID NO: 35; SEQ ID NO: 38; SEQ ID NO: 41; SEQ ID NO: 44; SEQ ID NO: 47; and SEQ ID NO: 49 Amino acid SEQ ID NO: 12; SEQ ID NO: 15; SEQ ID NO: sequences of ORF1 18; SEQ ID NO: 21; SEQ ID NO: 24; SEQ ID of Pong in rice NO: 27; SEQ ID NO: 30; SEQ ID NO: 33; SEQ ID NO: 36; SEQ ID NO: 39; SEQ ID NO: 42; SEQ ID NO: 45; and SEQ ID NO: 50 Amino acid SEQ ID NO: 13; SEQ ID NO: 16; SEQ ID NO: sequences of ORF2 19; SEQ ID NO: 22; SEQ ID NO: 25; SEQ ID in Pong in rice NO: 28; SEQ ID NO: 31; SEQ ID NO: 34; SEQ ID NO: 37; SEQ ID NO: 40; SEQ ID NO: 43; SEQ ID NO: 46; SEQ ID NO: 48; and SEQ ID NO: 51 Nucleotide sequences SEQ ID NO: 52; SEQ ID NO: 54; SEQ ID NO: of ORF2 in Pong in 56; SEQ ID NO: 58; SEQ ID NO: 62; SEQ ID Brassica NO: 64; SEQ ID NO: 66; SEQ ID NO: 68; and SEQ ID NO: 70 Amino acid sequences SEQ ID NO: 53; SEQ ID NO: 55; SEQ ID NO: of ORF2 in Pong in 57; SEQ ID NO: 59; SEQ ID NO: 61; SEQ ID Brassica NO: 63; SEQ ID NO: 65; SEQ ID NO: 67; SEQ ID NO: 69; and SEQ ID NO: 71 Nucleotide sequences SEQ ID NO: 72; SEQ ID NO: 74; SEQ ID NO: of ORF1 in Pong in 76; SEQ ID NO: 78; SEQ ID NO: 80; SEQ ID Brassica NO: 82; SEQ ID NO: 84; SEQ ID NO: 86; SEQ ID NO: 88; SEQ ID NO: 90 Amino acid SEQ ID NO: 73; SEQ ID NO: 75; SEQ ID NO: sequences of ORF1 77; SEQ ID NO: 79; SEQ ID NO: 81; SEQ ID in Pong in Brassica NO: 83; SEQ ID NO: 85; SEQ ID NO: 87; SEQ ID NO: 89; SEQ ID NO: 91

[0040] In preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:4; and homologs and orthologs thereof. In other preferred embodiments the PTE is selected from the group consisting of a polynucleotide as defined in SEQ ID NO:5; and homologs and orthologs thereof. In other preferred embodiments the PTE is selected from the group consisting of a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49; and homologs and orthologs thereof. In still other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and homologs and orthologs thereof. In other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 2) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and homologs and orthologs thereof. In still other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 2) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and homologs and orthologs thereof.

[0041] In other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 2) a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and orthologs and homologs thereof. In other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 2) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and homologs and orthologs thereof.

[0042] In still other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 2) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and homologs and orthologs thereof. In still other preferred embodiments, the PTE comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; 2) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and homologs and orthologs thereof.

[0043] As used herein, the term polypeptide refers to a chain of at least four amino acids joined by peptide bonds. The chain may be linear, branched, circular or combinations thereof. Accordingly, the present invention provides isolated PTPs selected from the group consisting of PONG_LIKE_(—)1, PONG_LIKE_(—)2, PONG_LIKE_(—)3, PONG_LIKE_(—)4, PONG_LIKE_(—)5a, PONG_LIKE_(—)5b, PONG_LIKE_(—)5c, PONG_LIKE_(—)6, PONG LIKE_(—)7, PONG_LIKE_(—)8, PONG_LIKE_(—)9, PONG_LIKE_(—)10, and PONG_LIKE_(—)12, and homologs thereof.

[0044] In preferred embodiments, the PTP is selected from: 1) a Oryza sativa ORF2 polypeptide as defined in SEQ ID NO:13; 2) an Oryza sativa PONG_LIKE_(—)1 ORF2 polypeptide as defined in SEQ ID NO:16; 3) an Oryza sativa PONG_LIKE_(—)2 ORF2 polypeptide as defined in SEQ ID NO:19; 4) an Oryza sativa PONG LIKE_(—)3 ORF2 polypeptide as defined in SEQ ID NO:22; 5) an Oryza sativa PONG_LIKE_(—)4 ORF2 polypeptide as defined in SEQ ID NO:25; 6) an Oryza sativa PONG_LIKE_(—)5a ORF2 polypeptide as defined in SEQ ID NO:28; 7) an Oryza sativa PONG_LIKE_(—)5b ORF2 polypeptide as defined in SEQ ID NO:31; 8) an Oryza sativa PONG_LIKE_(—)5c ORF2 polypeptide as defined in SEQ ID NO:34; 9) an Oryza saliva PONG_LIKE_(—)6 ORF2 polypeptide as defined in SEQ ID NO:37; 10) an Oryza sativa PONG_LIKE_(—)7 ORF2 polypeptide as defined in SEQ ID NO:40; 11) an Oryza sativa PONG_LIKE_(—)8 ORF2 polypeptide as defined in SEQ ID NO:43; 12) an Oryza sativa PONG_LIKE_(—)9 ORF2 polypeptide as defined in SEQ ID NO:46; 13) an Oryza sativa PONG_LIKE_(—)10 ORF2 polypeptide as defined in SEQ ID NO:48; and 14) an Oryza sativa PONG_LIKE_(—)12 ORF2 polypeptide as defined in SEQ ID NO:51, and homologs and orthologs thereof.

[0045] In one embodiment, the PTPs and PTEs of the present invention are produced by recombinant DNA techniques. For example, a nucleic acid molecule encoding the transposase polypeptide or a nucleic acid comprising a transposable element is cloned into a vector (as described below), the vector is introduced into a host cell (as described below) and the PTP is expressed in the host cell or the PTE may insert into the genome of the host cell. The PTP or PTE can then be isolated from the cells by an appropriate purification scheme using standard polypeptide purification techniques. For the purposes of the invention, the term “recombinant polynucleotide” refers to a polynucleotide that has been altered, rearranged or modified by genetic engineering. Examples include any cloned polynucleotide, and polynucleotides that are linked or joined to heterologous sequences. The term “recombinant” does not refer to alterations to polynucleotides that result from naturally occurring events, such as spontaneous mutations. Alternative to recombinant expression, a PTP, or peptide can be synthesized chemically using standard peptide synthesis techniques. Moreover, native PTPs can be isolated from cells (e.g., Oryza sativa, or Brassica oleracea), for example using an anti-PTP antibody, which can be produced by standard techniques utilizing a PTP or fragment thereof.

[0046] The invention further provides an isolated PTP-encoding nucleic acid. The present invention includes PTP-encoding nucleic acids that encode PTPs as described herein. In preferred embodiments, the PTP coding nucleic acid is selected from: 1) Nucleotide sequence of Pong in rice as defined in SEQ ID NO:8; 2) Nucleotide sequence of Pong in rice as defined in SEQ ID NO:9; 3) Nucleotide sequence of Pong in rice as defined in SEQ ID NO:10; 4) Nucleotide sequence of Pong in rice as defined in SEQ ID NO:11; 5) Nucleotide sequence of PONG_LIKE_(—)1 in Oryza sativa as defined in SEQ ID NO:14; 6) Nucleotide sequence of PONG_LIKE_(—)2 in Oryza sativa as defined in SEQ ID NO:17; 7) Nucleotide sequence of PONG_LIKE_(—)3 in Oryza sativa as defined in SEQ ID NO:20; 8) Nucleotide sequence of PONG_LIKE_(—)4 in Oryza sativa as defined in SEQ ID NO:23; 9) Nucleotide sequence of PONG_LIKE_(—)5a in Oryza sativa as defined in SEQ ID NO:26; 10) Nucleotide sequence of PONG_LIKE_(—)5b in Oryza sativa as defined in SEQ ID NO:29; 11) Nucleotide sequence of PONG_LIKE_(—)5c in Oryza sativa as defined in SEQ ID NO:32; 12) Nucleotide sequence of PONG_LIKE_(—)6 in Oryza sativa as defined in SEQ ID NO:35; 13) Nucleotide sequence of PONG_LIKE_(—)7 in Oryza sativa as defined in SEQ ID NO:38; 14) Nucleotide sequence of PONG_LIKE_(—)8 in Oryza sativa as defined in SEQ ID NO:41; 15) Nucleotide sequence of PONG_LIKE_(—)9 in Oryza sativa as defined in SEQ ID NO:44; 16) Nucleotide sequence of PONG_LIKE_(—)10 in Oryza sativa as defined in SEQ ID NO:47; and 17) Nucleotide sequence of PONG_LIKE_(—)12 in Oryza sativa as defined in SEQ ID NO:49, and homologs and orthologs thereof. Homologs and orthologs of the nucleotide sequences are defined below. In one preferred embodiment, the nucleic acid and polypeptide are isolated from the plant genus Brassica, or Oryza. In another preferred embodiment, the nucleic acid and polypeptide are from a Brassica oleracea plant, or an Oryza sativa plant.

[0047] As also used herein, the term “nucleic acid” and “polynucleotide” refer to RNA or DNA that is linear or branched, single or double stranded, or a hybrid thereof. The term also encompasses RNA/DNA hybrids. These terms also encompass untranslated sequence located at both the 3′ and 5′ ends of the coding region of the gene: at least about 1000 nucleotides of sequence upstream from the 5′ end of the coding region and at least about 200 nucleotides of sequence downstream from the 3′ end of the coding region of the gene. Less common bases, such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others can also be used for antisense, dsRNA and ribozyme pairing. For example, polynucleotides that contain C-5 propyne analogues of uridine and cytidine have been shown to bind RNA with high affinity and to be potent antisense inhibitors of gene expression. Other modifications, such as modification to the phosphodiester backbone, or the 2′-hydroxy in the ribose sugar group of the RNA can also be made. The antisense polynucleotides and ribozymes can consist entirely of ribonucleotides, or can contain mixed ribonucleotides and deoxyribonucleotides. The polynucleotides of the invention may be produced by any means, including genomic preparations, cDNA preparations, in vitro synthesis, RT-PCR, and in vitro or in vivo transcription.

[0048] An “isolated” nucleic acid molecule is one that is substantially separated from other nucleic acid molecules which are present in the natural source of the nucleic acid (i.e., sequences encoding other polypeptides). Preferably, an “isolated” nucleic acid is free of some of the sequences which naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in its naturally occurring replicon. For example, a cloned nucleic acid is considered isolated. In various embodiments, the isolated PTP or PTE nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived (e.g., a Brassica oleracea, or an Oryza sativa cell). A nucleic acid is also considered isolated if it has been altered by human intervention, or placed in a locus or location that is not its natural site, or if it is introduced into a cell by agroinfection. Moreover, an “isolated” nucleic acid molecule can be free from some of the other cellular material with which it is naturally associated, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized.

[0049] Specifically excluded from the definition of “isolated nucleic acids” are: naturally-occurring chromosomes (such as chromosome spreads), artificial chromosome libraries, genomic libraries, and cDNA libraries that exist either as an in vitro nucleic acid preparation or as a transfected/transformed host cell preparation, wherein the host cells are either an in vitro heterogeneous preparation or plated as a heterogeneous population of single colonies. Also specifically excluded are the above libraries wherein a specified nucleic acid makes up less than 5% of the number of nucleic acid inserts in the vector molecules. Further specifically excluded are whole cell genomic DNA or whole cell RNA preparations (including whole cell preparations that are mechanically sheared or enzymatically digested). Even further specifically excluded are the whole cell preparations found as either an in vitro preparation or as a heterogeneous mixture separated by electrophoresis wherein the nucleic acid of the invention has not further been separated from the heterologous nucleic acids in the electrophoresis medium (e.g., further separating by excising a single band from a heterogeneous band population in an agarose gel or nylon blot).

[0050] A nucleic acid molecule of the present invention can be isolated using standard molecular biology techniques and the sequence information provided herein. For example, a nucleic acid molecule comprising a nucleotide sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; comprising a nucleotide sequence of SEQ ID NO:5; comprising a nucleotide sequence of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; or a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of 1) a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; 2) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 3) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 4) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 5) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 6) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 7) a polynucleotide having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 8) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 9) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 10) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 11) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 12) a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; 13) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein.

[0051] In another example, a rice PTP nucleic acid can be isolated from a rice library using all or portion of one of the sequences of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, a PTP or PTE nucleic acid can be isolated from the genomic library of an organism using all of a portion of one of the sequences of SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; SEQ ID NO:90; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. Moreover, a nucleic acid molecule encompassing all or a portion of one of the sequences of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90 can be isolated by the polymerase chain reaction using oligonucleotide primers designed based upon this sequence. For example, mRNA can be isolated from plant cells (e.g., by the guanidinium-thiocyanate extraction procedure of Chirgwin et al., 1979, Biochemistry 18:5294-5299) and cDNA can be prepared using reverse transcriptase (e.g., Moloney MLV reverse transcriptase, available from Gibco/BRL, Bethesda, Md.; or AMV reverse transcriptase, available from Seikagaku America, Inc., St. Petersburg, Fla.). Synthetic oligonucleotide primers for polymerase chain reaction amplification can be designed based upon one of the nucleotide sequences shown in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90. A nucleic acid molecule of the invention can be amplified using cDNA or, alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid molecule so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to a PTP nucleotide sequence can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.

[0052] In a preferred embodiment, an isolated nucleic acid molecule of the invention comprises one of the nucleotide sequences shown in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49. These cDNAs may comprise sequences encoding the PTPs, (i.e., one of the “coding regions” of PONG_LIKE_(—)1 and PONG LIKE_(—)2), as well as 5′ untranslated sequences and 3′ untranslated sequences. The PTP coding region of PONG_LIKE_(—)1 comprises nucleotides 3,236-4,585 of SEQ ID NO:14 whereas the PTP coding region of PONG_LIKE_(—)2 comprises nucleotides 968-2,282 of SEQ ID NO:17. It is to be understood that SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49 comprise both coding regions for the transposase and 5′ and 3′ untranslated regions. Alternatively, the nucleic acid molecules of the present invention can comprise only the coding region of any of the sequences in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49 or can contain whole genomic fragments isolated from genomic DNA. The present invention also includes PTP coding nucleic acids that encode PTPs as described herein.

[0053] Moreover, the nucleic acid molecule of the invention can comprise a portion of the coding region of one of the sequences in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90 for example, a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of a PTP. The nucleotide sequences determined from the cloning of the PTP genes from Brassica oleracea, and Oryza sativa allow for the generation of probes and primers designed for use in identifying and/or cloning PTP homologs in other cell types and organisms, as well as PTP homologs from other related species. The portion of the coding region can also encode a biologically active fragment of a PTP.

[0054] As used herein, the term “biologically active portion of” a PTP is intended to include a portion, e.g., a domain/motif, of a PTP that participates in the transposition of a transposable element. For the purposes of the present invention, transposition of a transposable element refers to at least the movement of one transposable element in an organism. Methods for quantitating transposition are provided at least in Example 2 below.

[0055] The mPing/Pong transposable element may be actively transposing in a number of taxa other than rice and Brassica, i.e. the transposable element may transpose in eukaryotes under the appropriate conditions, thus, it will be recognized by those skilled in the art that the methods disclosed herein relating to plants may be extended to other higher eukaryotes. If the transposase is functional when expressed or otherwise introduced in vertebrate embryos or cells, it will be possible to develop transformation methods based on mPing/Pong elements for non-plant species as well.

[0056] Biologically active portions of a PTP include peptides comprising amino acid sequences derived from the amino acid sequence of a PTP, e.g., an amino acid sequence of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91 or the amino acid sequence of a polypeptide identical to a PTP, which include fewer amino acids than a full length PTP or the full length polypeptide which is identical to a PTP, and exhibit at least one activity of a PTP. Typically, biologically active portions (e.g., peptides which are, for example, 5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in length) comprise a domain or motif with at least one activity of a PTP. Moreover, other biologically active portions in which other regions of the polypeptide are deleted, can be prepared by recombinant techniques and evaluated for one or more of the activities described herein. Preferably, the biologically active portions of a PTP include one or more selected domains/motifs or portions thereof having biological activity such as a catalytic domain. For example, a catalytic domain of PONG_LIKE_(—)1 spans amino acid residues 199-341 of SEQ ID NO:16, and a catalytic domain of PONG_LIKE_(—)2 spans amino acid residues 193-335 of SEQ ID NO:19. Accordingly, the present invention includes PTPs comprising amino acid residues 199341 of SEQ ID NO:15 and amino acid residues 193-335 of SEQ ID NO:19.

[0057] The invention also provides PTP chimeric or fusion polypeptides. As used herein, a PTP “chimeric polypeptide” or “fusion polypeptide” comprises a PTP operatively linked to a non-PTP. A PTP polypeptide refers to a polypeptide having an amino acid sequence corresponding to a PTP, whereas a non-PTP polypeptide refers to a polypeptide having an amino acid sequence corresponding to a polypeptide which is not substantially identical to the PTP, e.g., a polypeptide that is different from the PTP and is derived from the same or a different organism. As used herein with respect to the fusion polypeptide, the term “operatively linked” is intended to indicate that the PTP and the non-PTP are fused to each other so that both sequences fulfill the proposed function attributed to the sequence used. The non-PTP can be fused to the N-terminus or C-terminus of the PTP. For example, in one embodiment, the fusion polypeptide is a GST-PTP fusion polypeptide in which the PTP sequences are fused to the C-terminus of the GST sequences. Such fusion polypeptides can facilitate the purification of recombinant PTPs. In another embodiment, the fusion polypeptide is a PTP containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of a PTP can be increased through use of a heterologous signal sequence.

[0058] Preferably, a PTP chimeric or fusion polypeptide of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and re-amplified to generate a chimeric gene sequence (See, e.g., Current Protocols in Molecular Biology, Eds. Ausubel et al John Wiley & Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A PTP-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the PTP.

[0059] Large amounts of the recombinant DNA molecules may be produced by replication in a suitable host cell. Natural or synthetic DNA fragments coding for a protein of interest are incorporated into recombinant polynucleotide constructs, typically DNA constructs, capable of introduction into and replication in a prokaryotic or eukaryotic cell, especially Escherichia coli or Saccharomyces cerevisiae. Commonly used prokaryotic hosts include strains of Escherichia coli, although other prokaryotes, such as Bacillus subtilis or a pseudomonad, may also be used. Eukaryotic host cells include yeast, filamentous fungi, plant, insect, amphibian and avian species. Such factors as ease of manipulation, ability to appropriately glycosylate expressed proteins, degree and control of protein expression, ease of purification of expressed proteins away from cellular contaminants or other factors influence the choice of the host cell.

[0060] In addition to fragments and fusion polypeptides of the PTPs described herein, the present invention includes homologs and analogs of naturally occurring PTPs and PTP-encoding nucleic acids, and of naturally occurring PTE nucleic acids. “Homologs” are defined herein as two nucleic acids or polypeptides that have similar, or substantially identical, nucleotide or amino acid sequences, respectively. Homologs include allelic variants, orthologs, paralogs, agonists and antagonists of PTPs as defined hereafter. The term “homolog” further encompasses nucleic acid molecules that differ from one of the nucleotide sequences shown in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70 (and portions thereof) due to degeneracy of the genetic code and thus encode the same PTP as that encoded by the nucleotide sequences shown in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. As used herein a “naturally occurring” PTP refers to a PTP amino acid sequence that occurs in nature. Preferably, a naturally occurring PTP comprises an amino acid sequence selected from the group consisting of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; and SEQ ID NO:91. Similarly, a “naturally occurring” PTE refers to a PTE nucleic acid sequence that occurs in nature. Preferably, a naturally occurring PTE comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49. In another embodiment, the naturally occurring PTE comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; and SEQ ID NO:90. In other embodiments, the naturally occurring PTE comprises a nucleic acid sequence selected from the group of polynucleotides encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and the group of polynucleotides encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0061] In other embodiments, the naturally occurring PTE comprises a nucleic acid sequence selected from the group consisting of 1) a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; 2) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 3) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 4) a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 5) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 6) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and 7) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. An agonist of the PTP can retain substantially the same, or a subset, of the biological activities of the PTP. An antagonist of the PTP can inhibit one or more of the activities of the naturally occurring form of the PTP.

[0062] Nucleic acid molecules corresponding to natural allelic variants and analogs, orthologs and paralogs of a PTP or PTE nucleic acid can be isolated based on their identity to the rice, or Brassica PTP and PTE nucleic acids described herein using PTP or PTE nucleic acid sequence, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent or moderate hybridization conditions. In an alternative embodiment, homologs of the PTP can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the PTP for PTP agonist or antagonist activity. In one embodiment, a variegated library of PTP variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of PTP variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential PTP sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion polypeptides (e.g., for phage display) containing the set of PTP sequences therein. There are a variety of methods that can be used to produce libraries of potential PTP homologs from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene is then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential PTP sequences. Methods for synthesizing degenerate oligonucleotides are known in the art. See, e.g., Narang, S. A., 1983, Tetrahedron 39:3; Itakura et al., 1984, Annu. Rev. Biochem. 53:323; Itakura et al., 1984, Science 198:1056; Ike et al., 1983, Nucleic Acid Res. 11:477.

[0063] In addition, libraries of fragments of the PTP coding regions can be used to generate a variegated population of PTP fragments for screening and subsequent selection of homologs of a PTP. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a PTP coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA, which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S1 nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal, and internal fragments of various sizes of the PTP.

[0064] Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of PTP homologs. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique that enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify PTP homologs (Arkin and Yourvan, 1992, PNAS 89:7811-7815; Delgrave et al., 1993, Polypeptide Engineering 6(3):327-331). In another embodiment, cell based assays can be exploited to analyze a variegated PTP library, using methods well known in the art. The present invention further provides a method of identifying a novel PTP, comprising (a) raising a specific antibody response to a PTP, or a fragment thereof, as described herein; (b) screening putative PTP material with the antibody, wherein specific binding of the antibody to the material indicates the presence of a potentially novel PTP; and (c) analyzing the bound material in comparison to known PTP, to determine its novelty.

[0065] As stated above, the present invention includes PTPs, PTEs and homologs and analogs thereof. To determine the percent sequence identity of two amino acid sequences (e.g., one of the sequences of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91, and a mutant form thereof), the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one polypeptide for optimal alignment with the other polypeptide or nucleic acid). The amino acid residues at corresponding amino acid positions are then compared. When a position in one sequence (e.g., one of the sequences of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91) is occupied by the same amino acid residue as the corresponding position in the other sequence (e.g., a mutant form of the sequence selected from the polypeptide of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91), then the molecules are identical at that position. The same type of comparison can be made between two nucleic acid sequences.

[0066] The percent sequence identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., percent sequence identity=numbers of identical positions/total numbers of positions×100). Preferably, the isolated amino acid homologs included in the present invention are at least about 25-30%, preferably at least 30-40%, and more preferably at least about 40-50%, 50-60%, 60-70%, 70-75%, 75-80%, 80-85%, 85-90% or 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more identical to an entire amino acid sequence shown in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. In yet another embodiment, the isolated amino acid homologs included in the present invention are at least about 25-30%, preferably at least 40-50%, and more preferably at least about 50-60%, 60-70%, 70-75%, 75-80%, 80-85%, 85-90% or 90-95%, and most preferably at least about 96%, 97%, 98%, 99% or more identical to an entire amino acid sequence encoded by a nucleic acid sequence shown in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In other embodiments, the PTP amino acid homologs have sequence identity over at least 15 contiguous amino acid residues, more preferably at least 25 contiguous amino acid residues, and most preferably at least 35 contiguous amino acid residues of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. In one embodiment of the present invention, the homolog has at least about 50-60%, preferably at least about 60-70%, more preferably at least about 70-75%, 75-80%, 80-85%, 85-90% or 90-95%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more sequence identity with the conserved region of ORF1 in Brassica oleracea (for example, amino acids 1-113 of SEQ ID NO:73) or the catalytic domain of ORF2 in Brassica oleracea (for example, amino acids 1-121 of SEQ ID NO:53).

[0067] In preferred embodiments, the PTP amino acid homologs of the present invention comprise an amino acid sequence selected from the group consisting of: 1) an amino acid encoded by a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; 2) a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 3) a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 4) a polypeptide encoded by a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 5) a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 6) a polypeptide encoded by a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and 7) a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0068] In another preferred embodiment, an isolated nucleic acid homolog of the invention comprises a nucleotide sequence which is at least about 40-50%, preferably at least about 50-60%, more preferably at least about 60-70%, 70-75%, 75-80%, 80-85%, 85-90% or 90-95%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more identical to a nucleotide sequence shown in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; and SEQ ID NO:49, or to a portion comprising at least 60 consecutive nucleotides thereof. The preferable length of sequence comparison for nucleic acids is at least 75 nucleotides, and more preferably at least 100 nucleotides. In a further embodiment, the isolated nucleic acid homolog of the invention comprises a nucleotide sequence which is at least 40-50%, preferably at least 50-60%, more preferably at least about 60-70%, 70-75%, 75-80%, 80-85%, 85-90% or 90-95%, and even more preferably at least about 95%, 96%, 97%, 98%, 99% or more identical to a nucleotide sequence as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; and SEQ ID NO:90.

[0069] In a preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49.

[0070] In a preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 2) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50 and homologs and orthologs thereof.

[0071] In another preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 2) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and homologs and orthologs thereof.

[0072] In another preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 2) a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and homologs and orthologs thereof.

[0073] In another preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 2) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and homologs and orthologs thereof.

[0074] In another preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 2) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and homologs and orthologs thereof.

[0075] In another preferred embodiment, the isolated nucleic acid of the invention comprises a transposable element capable of actively transposing, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; 2) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and homologs and orthologs thereof.

[0076] It is further preferred that a isolated nucleic acid homolog of the invention encodes a PTP, or portion thereof, that is at least 50% identical to an amino acid sequence of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51 and that functions as a modulator of translocation of a transposable element. In an additional preferred embodiment, the isolated nucleic acid homolog of the invention encodes a PTP, or portion thereof that is at least 75% identical to an amino acid sequence of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. In a further preferred embodiment, the nucleic acid homolog encodes a PTP that functions as a transposase.

[0077] For the purposes of the invention, the percent sequence identity between two nucleic acid or polypeptide sequences may be determined using the “Blast Two Sequences” program available at National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html). A gap opening penalty of 5 and a gap extension penalty of 2 are used for determining the percent identity of two nucleic acids. A gap opening penalty of 11 and a gap extension penalty of 1 are used for determining the percent identity of two polypeptides. All other parameters are set at the default settings. Multiple alignment was performed using the CLUSTALW program available at European Bioinformatics Institute (http://www.ebi.ac.uk/clustalw/), the gap opening penalty is 10, and the gap extension penalty is 0.05 with blosum62 matrix. It is to be understood that for the purposes of determining sequence identity when comparing a DNA sequence to an RNA sequence, a thymidine nucleotide is equivalent to a uracil nucleotide.

[0078] In another aspect, the invention provides an isolated nucleic acid comprising a polynucleotide that hybridizes to the polynucleotide of SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70 under moderate or highly stringent conditions. In another aspect, the invention provides an isolated nucleic acid comprising a polynucleotide that hybridizes under moderately or highly stringent conditions to a polynucleotide encoding a polypeptide of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. More particularly, an isolated nucleic acid molecule of the invention is at least 15 nucleotides in length and hybridizes under moderately or highly stringent conditions to the nucleic acid molecule comprising a nucleotide sequence of SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. Alternatively, an isolated nucleic acid molecule of the invention is at least 15 nucleotides in length and comprises a polynucleotide that hybridizes under moderate or stringent conditions to a nucleic acid sequence encoding a polypeptide of SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; SEQ ID NO:71; SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. In other embodiments, the nucleic acid is at least 30, 50, 100, 250 or more nucleotides in length.

[0079] In one embodiment, an isolated nucleic acid homolog of the invention comprises a nucleotide sequence which hybridizes under moderately stringent conditions to the nucleotide sequence shown in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, and functions as a modulator of translocation of a transposable element. In another embodiment, an isolated nucleic acid homolog of the invention comprises a nucleotide sequence which hybridizes under highly stringent conditions to the nucleotide sequence shown in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:0; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and is actively transposing.

[0080] Various degrees of stringency of hybridization can be employed for studies of cloned sequences isolated as described herein. The more stringent the conditions, the greater the complementarity that is required for duplex formation. Stringency can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under moderate to high stringency conditions by techniques well know in the art, as described, for example in Keller, G. H., M. M. Manak, 1987 DNA Probes, Stockton Press, New York, N.Y., pp. 169-170, hereby incorporated by reference. In a preferred embodiment, the hybridization is selective for target DNA. As used herein, the term “selective hybridization” or “selectively hybridizing” refers to the ability to discern between the binding of a nucleic acid sequence to a target DNA sequence as compared to other non-target DNA sequences.

[0081] As used herein, moderate to high stringency conditions for hybridization are conditions that achieve the same, or about the same, degree of specificity of hybridization as the conditions described herein. As used herein, the term “highly stringent” or “high stringency conditions” comprises hybridizing at 68° C. in 5×SSC/5× Denhardt's solution/0.1% SDS, and washing in 0.2×SSC/0.1% SDS at 65° C. As used herein, the term “moderately stringent” or “moderate stringency conditions” comprise hybridizing at 55° C. in 5×SSC/5× Denhardt's solution/0.1% SDS and washing at 42° C. in 3×SSC. The parameters of temperature and salt concentration can be varied to achieve the desired level of sequence identity between probe and target nucleic acid. See, e.g., Sambrook et al. 1989 Molecular Cloning, Second Edition, Cold Spring Harbor Laboratory, Plainview, N.Y. Ausubel et al., 1995 Current Protocols in Molecular Biology, John Wiley & Sons, NY, N.Y., Meinkoth and Wahl, 1984, Anal. Biochem. 138:267-284; or Tijssen, 1993, Laboratory Techniques in Biochemistry and Molecular Biology. Hybridization with Nucleic Acid Probes, Part I, Chapter 2, Elsevier, N.Y., for further guidance on hybridization conditions.

[0082] Specifically, hybridization of immobilized DNA in Southern blots with ³²P-labeled gene specific probes is performed by standard methods (Maniatis et al., 1982 Molecular Cloning, Cold Spring Harbor Laboratory, Plainview, N.Y.). In general, hybridization and subsequent washes are carried out under moderate to high stringency conditions that allowed for detection of target sequences with homology to a particular nucleic acid molecule of interest. For double-stranded DNA gene probes, hybridization can be carried out overnight at 20-25° C. below the melting temperature (Tm) of the DNA hybrid in 6×SSPE 5× Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz et al., 1983 Methods of Enzymology, R. Wu, L, Grossman and K Moldave (Eds) Academic Press, New York 100:266-285).

[0083] Tm=81.5° C.+16.6 Log[Na⁺]+0.41(+G+C)−0.61(% formamide)−600/length of duplex in base pairs.

[0084] Washes are typically carried out as follows: twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS (low stringency wash), and once at TM-20° C. for 15 minutes in 0.2×SSPE, 0.1% SDS (moderate stringency wash).

[0085] For oligonucleotide probes, hybridization is carried out overnight at 10-20° C. below the melting temperature (Tm) of the hybrid 6×SSPE, 5× Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. Tm for oligonucleotide probes is determined by the following formula: TM(° C.)=2(number T/A base pairs+4(number G/C base pairs) (Suggs et al., 1981 ICB--UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown (Ed.), Academic Press, New York, 23:683-693).

[0086] Washes are typically carried out as follows: twice at room temperature for 15 minutes 1×SSPE, 0.1% SDS (low stringency wash), and once at the hybridization temperature for 15 minutes in 1×SSPE, 0.1% SDS (moderate stringency wash).

[0087] In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used: Low, 1 or 2×SSPE, room temperature; Low, 1 or 2×SSPE, 42° C.; Moderate, 0.5× or 1×SSPE, 60° C.; and High, 0.1×SSPE, 65° C.

[0088] Preferably, an isolated nucleic acid molecule of the invention that hybridizes in 5×SSC at 55° C. to a transposable element comprising at least a portion of a nucleic acid comprising two terminal inverted repeat nucleic acid sequences, wherein the transposable element in actively transposing. In preferred embodiments, the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; 2) a polynucleotide as defined in SEQ ID NO:5; 3) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; 4) a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; 5) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 6) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; 7) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 8) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; 9) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 10) a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; 11) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 12) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; 13) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 14) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; 15) a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; 16) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and homologs and orthologs thereof.

[0089] In other embodiments, the invention provides for an isolated nucleic acid sequence that hybridizes in 5×SSC at 55° C. to a transposable element comprising a nucleic acid sequence as defined in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and that corresponds to a naturally occurring nucleic acid molecule. As used herein, a “naturally occurring” nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural polypeptide). In one embodiment, the nucleic acid encodes a naturally occurring Oryza, or Brassica oleracea PTE or PTP. In another embodiment, the isolated nucleic acid sequence does not correspond to a naturally occurring nucleic acid molecule.

[0090] Using the above-described methods, and others known to those of skill in the art, one of ordinary skill in the art can isolate homologs of the PTPs comprising amino acid sequences shown in, for example, SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71. One subset of these homologs are allelic variants. As used herein, the term “allelic variant” refers to a nucleotide sequence containing polymorphisms that lead to changes in the amino acid sequences of a PTP and that exist within a natural population (e.g., a plant species or variety). Such natural allelic variations can typically result in 1-5% variance in a PTP or PTE nucleic acid. Allelic variants can be identified by sequencing the nucleic acid sequence of interest in a number of different plants, or other organisms, which can be readily carried out by using hybridization probes to identify the same PTP or PTE genetic locus in those organisms. Any and all such nucleic acid variations and resulting amino acid polymorphisms or variations in a PTP or PTE that are the result of natural allelic variation and that do not alter the functional activity of a PTP or PTE, are intended to be within the scope of the invention.

[0091] Moreover, nucleic acid molecules encoding PTPs and PTE nucleic acids from the same or other species such as PTP or PTE analogs, orthologs, and paralogs, are intended to be within the scope of the present invention. As used herein, the term “analogs” refers to two nucleic acid sequences that have the same or similar function, but that have evolved separately in unrelated organisms. As used herein, the term “orthologs” refers to two nucleic acids from different species, but that have evolved from a common ancestral gene by speciation. Normally, orthologs encode polypeptides having the same or similar functions. As also used herein, the term “paralogs” refers to two nucleic acids that are related by duplication within a genome. Paralogs usually have different functions, but these functions may be related (Tatusov, R. L. et al., 1997, Science 278(5338):631-637). Analogs, orthologs and paralogs of a naturally occurring PTP can differ from the naturally occurring PTP by post-translational modifications, by amino acid sequence differences, or by both. Post-translational modifications include in vivo and in vitro chemical derivatization of polypeptides, e.g., acetylation, carboxylation, phosphorylation, or glycosylation, and such modifications may occur during polypeptide synthesis or processing or following treatment with isolated modifying enzymes. In particular, orthologs of the invention will generally exhibit at least 80-85%, more preferably, 85-90% or 90-95%, and most preferably 95%, 96%, 97%, 98% or even 99% identity or sequence identity with all or part of a naturally occurring PTP amino acid sequence and will exhibit a function similar to a PTP. Preferably, a PTP ortholog of the present invention functions as a modulator of transposition of a transposable element. More preferably, a PTP ortholog modulates the transposition of mPing, Ping or Pong. In another embodiment, the PTP orthologs maintain the ability to participate in the transposition of a transposable element having homology to mPing, Ping or Pong in an organism. In a preferred embodiment, that organism is a plant.

[0092] In addition to naturally-occurring variants of a PTP sequence that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into a nucleotide sequence comprising the polynucleotide of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, thereby leading to changes in the amino acid sequence of the encoded PTP, without altering the functional activity of the PTP. For example, nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in a sequence comprising the polynucleotide of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of one of the PTPs without altering the activity of said PTP, whereas an “essential” amino acid residue is required for PTP activity. Other amino acid residues, however, (e.g., those that are not conserved or only semi-conserved in the domain having PTP activity) may not be essential for activity and thus are likely to be amenable to alteration without altering PTP activity.

[0093] Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding PTPs that contain changes in amino acid residues that are not essential for PTP activity. Such PTPs differ in amino acid sequence from a sequence contained in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71, yet retain at least one of the PTP activities described herein. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a polypeptide, wherein the polypeptide comprises an amino acid sequence at least about 50% identical to an amino acid sequence of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. Preferably, the polypeptide encoded by the nucleic acid molecule is at least about 50-60% identical to one of the sequences of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51, more preferably at least about 60-70% identical to one of the sequences of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51, even more preferably at least about 70-75%, 75-80%, 80-85%, 85-90%, 90-95% identical to one of the sequences of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51, and most preferably at least about 96%, 97%, 98%, or 99% identical to one of the sequences of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a polypeptide, wherein the polypeptide comprises an amino acid sequence at least about 50% identical to an amino acid sequence of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. Preferably, the polypeptide encoded by the nucleic acid molecule is at least about 50-60% identical to one of the sequences of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71, more preferably at least about 60-70% identical to one of the sequences of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71, even more preferably at least about 70-75%, 75-80%, 80-85%, 85-90%, 90-95% identical to one of the sequences of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71, and most preferably at least about 96%, 97%, 98%, or 99% identical to one of the sequences of SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. The preferred PTP homologs of the present invention participate in the transposition of a transposable element within the genome of an organism.

[0094] An isolated nucleic acid molecule encoding a PTP having sequence identity with a polypeptide sequence of SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71 can be created by introducing one or more nucleotide substitutions, additions or deletions into a nucleotide sequence of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, respectively, such that one or more amino acid substitutions, additions, or deletions are introduced into the encoded polypeptide. Mutations can be introduced into one of the sequences of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.

[0095] Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a PTP is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a PTP coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for a PTP activity described herein to identify mutants that retain PTP activity. Following mutagenesis of one of the sequences of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, the encoded polypeptide can be expressed recombinantly and the activity of the polypeptide can be determined by analyzing the transposition of a member of the mPing/Pong family of transposable elements in a plant expressing the polypeptide.

[0096] Additionally, optimized PTP nucleic acids can be created. As used herein, “optimized” refers to a nucleic acid that is genetically engineered to increase its expression in a given organism, or to increase its activity in a given organism. For example, to provide plant optimized PTP nucleic acids, the DNA sequence of the gene can be modified to 1) comprise codons preferred by highly expressed plant genes; 2) comprise an A+T content in nucleotide base composition to that substantially found in plants; 3) form a plant initiation sequence; or 4) eliminate sequences that cause destabilization, inappropriate polyadenylation, degradation, and termination of RNA, or that form secondary structure hairpins or RNA splice sites. Increased expression of PTP nucleic acids in plants can be achieved by utilizing the distribution frequency of codon usage in plants in general or a particular plant. Methods for optimizing nucleic acid expression in plants can be found in EPA 0359472; EPA 0385962; PCT Application No. WO 91/16432; U.S. Pat. No. 5,380,831; U.S. Pat. No. 5,436,391; Perlack et al., 1991, Proc. Natl. Acad. Sci. USA 88:3324-3328; and Murray et al., 1989, Nucleic Acids Res. 17:477-498. Similarly, optimized PTP nucleic acids can be generated for animals or fungi.

[0097] As used herein, “frequency of preferred codon usage” refers to the preference exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. To determine the frequency of usage of a particular codon in a gene, the number of occurrences of that codon in the gene is divided by the total number of occurrences of all codons specifying the same amino acid in the gene. Similarly, the frequency of preferred codon usage exhibited by a host cell can be calculated by averaging frequency of preferred codon usage in a large number of genes expressed by the host cell. It is preferable that this analysis be limited to genes that are highly expressed by the host cell. The percent deviation of the frequency of preferred codon usage for a synthetic gene from that employed by a host cell is calculated first by determining the percent deviation of the frequency of usage of a single codon from that of the host cell followed by obtaining the average deviation over all codons. As defined herein, this calculation includes unique codons (i.e., ATG and TGG). In general terms, the overall average deviation of the codon usage of an optimized gene from that of a host cell is calculated using the equation 1A=n=1 Z Xn−Yn Xn times 100 Z where Xn=frequency of usage for codon n in the host cell; Yn=frequency of usage for codon n in the synthetic gene; n represents an individual codon that specifies an amino acid; and the total number of codons is Z. The overall deviation of the frequency of codon usage, A, for all amino acids should preferably be less than about 25%, and more preferably less than about 10%.

[0098] Hence, a PTP-encoding nucleic acid can be optimized such that its distribution frequency of codon usage deviates, preferably, no more than 25% from that of highly expressed plant genes and, more preferably, no more than about 10%. In addition, consideration is given to the percentage G+C content of the degenerate third base (monocotyledons appear to favor G+C in this position, whereas dicotyledons do not). It is also recognized that the XCG (where X is A, T, C, or G) nucleotide is the least preferred codon in dicots whereas the XTA codon is avoided in both monocots and dicots. Optimized PTP nucleic acids of this invention also preferably have CG and TA doublet avoidance indices closely approximating those of the chosen host plant (i.e., Oryza, or Brassica oleracea). More preferably these indices deviate from that of the host by no more than about 10-15%.

[0099] In addition to the nucleic acid molecules encoding the PTPs described above, another aspect of the invention pertains to isolated nucleic acid molecules that are antisense thereto. Antisense polynucleotides are thought to inhibit gene expression of a target polynucleotide by specifically binding the target polynucleotide and interfering with transcription, splicing, transport, translation, and/or stability of the target polynucleotide. Methods are described in the prior art for targeting the antisense polynucleotide to the chromosomal DNA, to a primary RNA transcript, or to a processed mRNA. Preferably, the target regions include splice sites, translation initiation codons, translation termination codons, and other sequences within the open reading frame.

[0100] The term “antisense,” for the purposes of the invention, refers to a nucleic acid comprising a polynucleotide that is sufficiently complementary to all or a portion of a gene, primary transcript, or processed mRNA, so as to interfere with expression of the endogenous gene. “Complementary” polynucleotides are those that are capable of base pairing according to the standard Watson-Crick complementarity rules. Specifically, purines will base pair with pyrimidines to form a combination of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of DNA, or adenine paired with uracil (A:U) in the case of RNA. It is understood that two polynucleotides may hybridize to each other even if they are not completely complementary to each other, provided that each has at least one region that is substantially complementary to the other. The term “antisense nucleic acid” includes single stranded RNA as well as double-stranded DNA expression cassettes that can be transcribed to produce an antisense RNA. “Active” antisense nucleic acids are antisense RNA molecules that are capable of selectively hybridizing with a primary transcript or mRNA encoding a polypeptide having at least 50% sequence identity with the polypeptide of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70.

[0101] The antisense nucleic acid can be complementary to an entire PTP coding strand, or to only a portion thereof. In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding a PTP. The term “coding region” refers to the region of the nucleotide sequence comprising codons that are translated into amino acid residues (e.g., the entire coding region of PONG_LIKE_(—)1 transposase comprises nucleotides 3,236-4,588 of SEQ ID NO:14, and the entire coding region of PONG_LIKE_(—)2 transposase comprises nucleotides 965-2,282 of SEQ ID NO:17). In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence encoding a PTP. The term “noncoding region” refers to 5′ and 3′ sequences that flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions). The antisense nucleic acid molecule can be complementary to the entire coding region of PTP mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of PTP mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of PTP mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. Typically, the antisense molecules of the present invention comprise an RNA having 60-100% sequence identity with at least 14 consecutive nucleotides of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, or a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; SEQ ID NO:51; SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. Preferably, the sequence identity will be at least 50%, more preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98% and most preferably 99%.

[0102] An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

[0103] In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual α-units, the strands run parallel to each other (Gaultier et al., 1987, Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (Inoue et al., 1987, Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al., 1987, FEBS Lett. 215:327-330).

[0104] The antisense nucleic acid molecules of the invention are typically administered to a cell or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a PTP to thereby inhibit expression of the polypeptide, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix. The antisense molecule can be modified such that it specifically binds to a receptor or an antigen expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecule to a peptide or an antibody which binds to a cell surface receptor or antigen. The antisense nucleic acid molecule can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong prokaryotic, viral, or eukaryotic (including plant) promoter are preferred.

[0105] As an alternative to antisense polynucleotides, ribozymes, sense polynucleotides, or double stranded RNA (dsRNA) can be used to reduce expression of a PTP polypeptide. By “ribozyme” is meant a catalytic RNA-based enzyme with ribonuclease activity which is capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which it has a complementary region. Ribozymes (e.g., hammerhead ribozymes described in Haselhoff and Gerlach, 1988, Nature 334:585-591) can be used to catalytically cleave PTP mRNA transcripts to thereby inhibit translation of PTP mRNA. A ribozyme having specificity for a PTP-encoding nucleic acid can be designed based upon the nucleotide sequence of a PTP cDNA, as disclosed herein (i.e., SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70,) or on the basis of a heterologous sequence to be isolated according to methods taught in this invention. For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a PTP-encoding mRNA. See, e.g., U.S. Pat. Nos. 4,987,071 and 5,116,742 to Cech et al. Alternatively, PTP mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J. W., 1993, Science 261:1411-1418. In preferred embodiments, the ribozyme will contain a portion having at least 7, 8, 9, 10, 12, 14, 16, 18 or 20 nucleotides, and more preferably 7 or 8 nucleotides, that have 100% complementarity to a portion of the target RNA. Methods for making ribozymes are known to those skilled in the art. See, e.g., U.S. Pat. Nos. 6,025,167; 5,773,260; and 5,496,698.

[0106] The term “dsRNA,” as used herein, refers to RNA hybrids comprising two strands of RNA. The dsRNAs can be linear or circular in structure. In a preferred embodiment, dsRNA is specific for a polynucleotide of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, or a polynucleotide having at least 70% sequence identity with SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. The hybridizing RNAs may be substantially or completely complementary. By “substantially complementary,” is meant that when the two hybridizing RNAs are optimally aligned using the BLAST program as described above, the hybridizing portions are at least 95% complementary. Preferably, the dsRNA will be at least 100 base pairs in length. Typically, the hybridizing RNAs will be of identical length with no over hanging 5′ or 3′ ends and no gaps. However, dsRNAs having 5′ or 3′ overhangs of up to 100 nucleotides may be used in the methods of the invention.

[0107] As used herein, “complement” and “complementary” refer to the ability of two single stranded nucleic acid fragments to base pair with each other, where an adenine on one nucleic acid fragment will base pair to a thymine on a second nucleic acid fragment and a cytosine on one nucleic acid fragment will base pair to a guanine on a second nucleic acid fragment. Two nucleic acid fragments are complementary to each other when a nucleotide sequence in one nucleic acid fragment can base pair with a nucleotide sequence in a second nucleic acid fragment. For instance, 5′-ATGC and 5′-GCAT are complementary. The term complement and complementary also encompasses two nucleic acid fragments where one nucleic acid fragment contains at least one nucleotide that will not base pair to at least one nucleotide present on a second nucleic acid fragment. For instance the third nucleotide of each of the two nucleic acid fragments 5′-ATTGC and 5′-GCTAT will not base pair, but these two nucleic acid fragments are complementary as defined herein. Typically two nucleic acid fragments are complementary if they hybridize under the conditions referred to herein.

[0108] The dsRNA may comprise ribonucleotides or ribonucleotide analogs, such as 2′-O-methyl ribosyl residues, or combinations thereof. See, e.g., U.S. Pat. Nos. 4,130,641 and 4,024,222. A dsRNA polyriboinosinic acid:polyribocytidylic acid is described in U.S. Pat. No. 4,283,393. Methods for making and using dsRNA are known in the art. One method comprises the simultaneous transcription of two complementary DNA strands, either in vivo, or in a single in vitro reaction mixture. See, e.g., U.S. Pat. No. 5,795,715. In one embodiment, dsRNA can be introduced into a plant or plant cell directly by standard transformation procedures. Alternatively, dsRNA can be expressed in a plant cell by transcribing two complementary RNAs.

[0109] Other methods for the inhibition of endogenous gene expression, such as triple helix formation (Moser et al., 1987, Science 238:645-650 and Cooney et al., 1988, Science 241:456-459) and co-suppression (Napoli et al., 1990, Plant Cell 2:279-289) are known in the art. Partial and full-length cDNAs have been used for the co-suppression of endogenous plant genes. See, e.g., U.S. Pat. Nos. 4,801,340, 5,034,323, 5,231,020, and 5,283,184; Van der Kroll et al., 1990, Plant Cell 2:291-299; Smith et al., 1990, Mol. Gen. Genetics 224:477-481 and Napoli et al., 1990, Plant Cell 2:279-289.

[0110] For sense suppression, it is believed that introduction of a sense polynucleotide blocks transcription of the corresponding target gene. The sense polynucleotide will have at least 65% sequence identity with the target plant gene or RNA. Preferably, the percent identity is at least 80%, 90%, 95% or more. The introduced sense polynucleotide need not be full length relative to the target gene or transcript. Preferably, the sense polynucleotide will have at least 65% sequence identity with at least 100 consecutive nucleotides of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. The regions of identity can comprise introns and and/or exons and untranslated regions. The introduced sense polynucleotide may be present in the plant cell transiently, or may be stably integrated into a plant chromosome or extrachromosomal replicon.

[0111] Alternatively, PTP gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of a PTP nucleotide sequence (e.g., a PTP promoter and/or enhancer) to form triple helical structures that prevent transcription of a PTP gene in target cells. See generally, Helene, C., 1991, Anticancer Drug Des. 6(6):569-84; Helene, C. et al., 1992, Ann. N.Y. Acad. Sci. 660:27-36; and Maher, L. J., 1992, Bioassays 14(12):807-15.

[0112] In addition to the PTP nucleic acids and polypeptides described above, the present invention encompasses these nucleic acids and polypeptides attached to a moiety. These moieties include, but are not limited to, detection moieties, hybridization moieties, purification moieties, delivery moieties, reaction moieties, binding moieties, and the like. A typical group of nucleic acids having moieties attached are probes and primers. Probes and primers typically comprise a substantially isolated oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 40, 50 or 75 consecutive nucleotides of a sense strand of one of the sequences set forth in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; an anti-sense sequence of one of the sequences set forth in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; or naturally occurring mutants thereof. Primers based on a nucleotide sequence of SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49; SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70, can be used in PCR reactions to clone PTP and PTE homologs. Probes based on the PTP nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or substantially identical polypeptides. In preferred embodiments, the probe further comprises a label group attached thereto, e.g. the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a genomic marker test kit for identifying cells which express a PTP, such as by measuring a level of a PTP-encoding nucleic acid, in a sample of cells, e.g., detecting PTP mRNA levels or determining whether a genomic PTP gene has been mutated or deleted.

[0113] Such probes may also be used to detect whether a cell contains a PTE, such as by transposon display, or screening a genomic library. Detection of a PTE can comprise using a probe that comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to the transposable element and detecting hybridization, thereby identifying the transposable element. In one embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide as defined in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; or SEQ ID NO:4. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50. In another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment, the transposable element comprises a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90. In another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. In another embodiment, the transposable element comprises a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. In another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0114] Such probes can also be used to determine whether a transposition of a transposable element has occurred in a sample or a cell. As used herein, the term “transposition” refers to the change in location of a transposable element in the genome of an organism. Such a transposition can be detected by a number of techniques currently known, or known in the future. One such preferred well-known technique for determining whether a transposition of a transposable element has occurred within a sample, a cell, or an organism is transposon display.

[0115] The present invention encompasses a method of screening a cell for a transposition of a transposable element, wherein the transposable element is actively transposing, comprising the steps of a) providing a cell comprising a transposable element, b) inducing a transposition of the transposable element by a transposase encoded by a nucleic acid sequence selected from the group consisting of: i) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; ii) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; iii) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and iv) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and c) comparing the phenotype of the cell containing the transposition of the transposable element to a wild-type cell not containing the transposition of the transposable element to thereby screen for a cell containing the transposition.

[0116] In one embodiment of the above method, the transposase is encoded by a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 75% identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In another embodiment, the transposase is encoded by a nucleic acid sequence selected from the group consisting of a polynucleotide encoding a polypeptide having at least 75% identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. 101141 In another embodiment of the above method, the transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide as defined in SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; or SEQ ID NO:4. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of a nucleic acid having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and 2) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and 2) a nucleic acid encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of: 1) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and 2) a nucleic acid having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of: 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and 2) a nucleic acid encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of: 1) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and 2) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. In another embodiment, the transposable element comprises a nucleic acid sequence selected from the group consisting of: 1) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and 2) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0117] The present invention further contemplates a method of localizing a transposable element nucleic acid sequence, comprising a) providing the genomic DNA of a cell; b) obtaining the nucleic acid sequence of the transposable element nucleic acid sequence and the adjacent genomic DNA, wherein the transposable element nucleic acid sequence comprises a polynucleotide selected from the group consisting of: i) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; ii) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; iii) a polynucleotide comprising at least 20 consecutive nucleotides of any of i) through ii) above; and iv) a polynucleotide complementary to a polynucleotide of any of i) through iii) above; to thereby localize the transposable element nucleic acid sequence. In one embodiment of the above method, the transposable element comprises a polynucleotide encoding a polypeptide having at least 95% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide having at least 90% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In yet another embodiment, the transposable element comprises a polynucleotide encoding a polypeptide having at least 80% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; SEQ ID NO:50; SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51.

[0118] In one embodiment of the above method, the cell is not transgenic. In another embodiment, the cell is transgenic. In a further embodiment of the above method, obtaining the nucleic acid sequence of the transposable element nucleic acid sequence and the adjacent DNA comprises performing transposon display. In a preferred embodiment, transposon display is performed as described in U.S. Pat. No. 6,420,117, herein incorporated by reference in its entirety. Preferably, performing transposon display to detect a transposition of a transposable element of the mPing/Pong family of DNA transposable elements comprises the use of one or more nucleic acid sequences selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:92; SEQ ID NO:93; SEQ ID NO:98; or SEQ ID NO:99; b) a polynucleotide having a nucleic acid sequence which hybridizes to the nucleic acid sequence of SEQ ID NO:1; SEQ ID NO:2; SEQ ID NO:3; SEQ ID NO:4; SEQ ID NO:5; SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; in 5×SSC at 55° C. and c) a polynucleotide having a nucleic acid sequence which hybridizes to the nucleic acid sequence of SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; SEQ ID NO:70; SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90 in 5×SSC at 55° C.

[0119] The present invention contemplates a method for making a transgenic cell, comprising transforming a cell with an isolated transposable element, wherein the isolated transposable element comprises a nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:4; b) a polynucleotide as defined SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; c) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and d) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71 and orthologs and homologs thereof.

[0120] In a preferred embodiment of the above method, the isolated transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 75% identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. In another preferred embodiment of the above method, the isolated transposable element comprises a nucleic acid sequence selected from the group consisting of a polynucleotide encoding a polypeptide having at least 75% identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0121] In alternative embodiments, the isolated transposable element comprises a nucleic acid sequence that hybridizes in 5×SSC at 55° C. to any of the polynucleotides as defined above. In other embodiments, the isolated transposable element is modified to include a promoter operatively linked to a foreign nucleic acid flanked by the terminal inverted repeats of the transposable element.

[0122] In certain embodiments of the above method, the cell transformed with the isolated transposable element further comprises a transposase protein encoded by a nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; b) a polynucleotide having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; c) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; d) a polynucleotide encoding a polypeptide having at least 90% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; e) a polynucleotide encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; f) a polynucleotide encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; g) a polynucleotide as defined SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; h) a polynucleotide having at least 90% sequence identity with a polynucleotide as defined SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; i) a polynucleotide having at least 75% sequence identity with a polynucleotide as defined SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; j) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; k) a polynucleotide encoding a polypeptide having at least 90% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and 1) a polynucleotide encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71.

[0123] The present invention further encompasses a transposase protein comprising a nucleic acid sequence selected from the group consisting of 1) a polynucleotide which hybridizes in 5×SSC at 55° C. to the polynucleotide as defined in any of a) through 1) above, and 2) a polynucleotide complementary to the polynucleotide as defined in 1).

[0124] In another preferred embodiment, the cell transformed with the isolated transposable element further comprises an isolated nucleic acid sequence encoding a transposase protein, wherein the nucleic acid sequence is selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; b) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; c) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and d) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. In one embodiment, the cell transformed with the isolated transposable element further comprises an isolated nucleic acid sequence encoding a transposase protein, wherein the nucleic acid sequence is selected from the group consisting of a polynucleotide having at least 75% identity with a polynucleotide as defined SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70. In another embodiment, the cell transformed with the isolated transposable element further comprises an isolated nucleic acid sequence encoding a transposase protein, wherein the nucleic acid sequence is selected from the group consisting of a polynucleotide encoding a polypeptide having at least 75% identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. 101231 In certain embodiments of the above method, the cell transformed with the isolated transposable element further comprises a transposase protein encoded by an isolated nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; b) a polynucleotide having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; c) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; d) a polynucleotide encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; e) a polynucleotide as defined SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; f) a polynucleotide having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70;; g) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and h) a polynucleotide encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71. The present invention further encompasses a transposase protein comprising an isolated nucleic acid sequence selected from the group consisting of a) a polynucleotide which hybridizes in 5×SSC at 55° C. to the polynucleotide as defined in any of a) through g) above, and b) a polynucleotide complementary to the polynucleotide as defined in a).

[0125] In a preferred embodiment of the above method, the isolated transposable element and nucleic acid sequence encoding the transposase protein are incorporated into a vector.

[0126] The present invention further contemplates a method for making a transgenic cell, comprising transforming a cell with transposase protein comprising an isolated nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; b) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; c) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and d) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and homologs and orthologs thereof.

[0127] In one embodiment of the above method the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 95% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 90% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 80% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 70% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51.

[0128] In another embodiment of the above method, the nucleic acid sequence comprises a polynucleotide having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In another embodiment, the nucleic acid sequence comprises a polynucleotide encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71.

[0129] In another embodiment of the above method, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and b) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment of the above method, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70; and b) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71.

[0130] In still another embodiment of the above method, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 95% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide encoding a polypeptide having at least 95% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide encoding a polypeptide having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51.

[0131] In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 95% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a polynucleotide having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; and SEQ ID NO:70. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 95% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71. In another embodiment, the nucleic acid sequence is a polynucleotide which hybridizes in 5×SSC at 55° C. to a nucleic acid sequence selected from the group consisting of a nucleic acid encoding a polypeptide having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; and SEQ ID NO:71.

[0132] The present invention provides a transgenic plant cell transformed by a PTP coding nucleic acid, wherein expression of the nucleic acid sequence in the plant cell results in increased transposition of a transposable element as compared to a wild type variety of the plant cell. In a preferred embodiment, the increase of transposition is 2 fold, more preferably the increase in transposition is 4-fold, and most preferably the increase in transposition is at least 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, or 1000-fold. The present invention further provides for a transgenic plant cell transformed by a PTE nucleic acid, wherein the PTE nucleic acid is capable of active transposition within the genome of the plant cell. The invention further provides transgenic plant parts and transgenic plants containing the plant cells described herein. In preferred embodiments, the transgenic plants and plant parts have increased transposition of a transposable element as compared to a wild type variety of the plant. Plant parts include, but are not limited to, stems, roots, ovules, stamens, leaves, embryos, meristematic regions, callus tissue, gametophytes, sporophytes, pollen, microspores, and the like. Plant cells include germ cells and somatic cells. In one embodiment, the transgenic plant is male sterile. Also provided is a plant seed produced by a transgenic plant transformed by a PTP coding nucleic acid or PTE nucleic acid wherein the seed contains the PTP coding nucleic acid or PTE nucleic acid, and wherein the plant is true breeding for increased transposition of a transposable element as compared to a wild type variety of the plant. The invention further provides a seed produced by a transgenic plant expressing a PTP, wherein the seed contains the PTP, and wherein the plant is true breeding for increased transposition of a transposable element as compared to a wild type variety of the plant. The invention also provides an agricultural product produced by any of the below-described transgenic plants, plant parts, and plant seeds. Agricultural products include, but are not limited to, plant extracts, proteins, amino acids, carbohydrates, fats, oils, polymers, vitamins, and the like. In other embodiments of the present invention, the plant cell, plant part or plant containing a PTP or PTE is not transgenic.

[0133] It is expected that an individual that contains transposable elements in its genome can be used in the present invention. The individual can be an animal, plant, or a fungi, and is preferably a plant. The plant can be a monocot plant or a dicot plant. Seeds and plants comprising a nucleic acid molecule as described are also preferred. More preferred are plants as described, wherein the plant is selected from the group consisting of: soybean; maize; sugar cane; beet; tobacco; wheat; barley; poppy; rape; sunflower; alfalfa; sorghum; rose; carnation; gerbera; carrot; tomato; lettuce; chicory; pepper; melon; cabbage; oat; rye; cotton; millet; flax; potato; pine; walnut; citrus (including oranges, grapefruit etc.); hemp; oak; rice; petunia; orchids; Arabidopsis; broccoli; cauliflower; brussel sprouts; onion; garlic; leek; squash; pumpkin; celery; pea; bean (including various legumes); strawberries; grapes; apples; cherries; pears; peaches; banana; palm; cocoa; cucumber; pineapple; apricot; plum; sugar beet; lawn grasses; maple; teosinte; Tripsacum; Coix; triticale; safflower; peanut; and olive. Most preferably, the plant is selected from the group consisting of rice and Brassica. Preferably, when the methods are directed to detecting a polymorphism between the nucleic acid fragments of two individuals, or directed to correlating the presence of an amplified fragment to a phenotype, the two individuals are the same species.

[0134] In certain embodiments of the present invention, the methods comprise an intermediate step of producing a progeny plant from a plant cell prior to analyzing the phenotype of the cell. As used herein, “phenotype” is a visible or otherwise measurable property of an individual.

[0135] As used herein, the term “variety” refers to a group of plants within a species that share constant characters that separate them from the typical form and from other possible varieties within that species. While possessing at least one distinctive trait, a variety is also characterized by some variation between individuals within the variety, based primarily on the Mendelian segregation of traits among the progeny of succeeding generations. A variety is considered “true breeding” for a particular trait if it is genetically homozygous for that trait to the extent that, when the true-breeding variety is self-pollinated, a significant amount of independent segregation of the trait among the progeny is not observed. In the present invention, the trait arises from the transgenic expression of one or more DNA sequences introduced into a plant variety.

[0136] In particular, a useful method to ascertain the level of transcription of the gene (an indicator of the amount of mRNA available for translation to the gene product) is to perform a Northern blot. For reference, see, for example, Ausubel et al., 1988, Current Protocols in Molecular Biology, Wiley: New York. The information from a Northern blot at least partially demonstrates the degree of transcription of the transformed gene. Total cellular RNA can be prepared from cells, tissues or organs by several methods, all well-known in the art, such as that described in Bormann, E. R. et al., 1992, Mol. Microbiol. 6:317-326. To assess the presence or relative quantity of polypeptide translated from this mRNA, standard techniques, such as a Western blot, may be employed. These techniques are well known to one of ordinary skill in the art. See, for example, Ausubel et al., 1988, Current Protocols in Molecular Biology, Wiley: New York.

[0137] The invention further provides an isolated recombinant expression vector comprising a PTP nucleic acid or PTE nucleic acid as described above, wherein expression of the vector in a host cell results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the host cell. As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid,” which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “expression vectors.” In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses, and adeno-associated viruses), which serve equivalent functions.

[0138] The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. As used herein with respect to a recombinant expression vector, “operatively linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term “regulatory sequence” is intended to include promoters, enhancers, and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) and Gruber and Crosby, in: Methods in Plant Molecular Biology and Biotechnology, Eds. Glick and Thompson, Chapter 7, 89-108, CRC Press: Boca Raton, Fla., including the references therein. Regulatory sequences include those that direct constitutive expression of a nucleotide sequence in many types of host cells and those that direct expression of the nucleotide sequence only in certain host cells or under certain conditions. It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of polypeptide desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce polypeptides or peptides, including fusion polypeptides or peptides, encoded by nucleic acids as described herein (e.g., PTPs, mutant forms of PTPs, fusion polypeptides, etc.).

[0139] The recombinant expression vectors of the invention can be designed for expression of PTPs in prokaryotic or eukaryotic cells. For example, PTP genes can be expressed in bacterial cells such as C. glutamicum, insect cells (using baculovirus expression vectors), yeast and other fungal cells (See Romanos, M. A. et al., 1992, Foreign gene expression in Yeast: a Review, Yeast 8:423-488; van den Hondel, C. A. M. J. J. et al., 1991, Heterologous gene expression in filamentous fungi, in: More Gene Manipulations in Fungi, J. W. Bennet & L. L. Lasure, eds., p. 396-428: Academic Press: San Diego; and van den Hondel, C. A. M. J. J. & Punt, P. J., 1991, Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, Peberdy, J. F. et al., eds., p. 1-28, Cambridge University Press: Cambridge), algae (Falciatore et al., 1999, Marine Biotechnology 1(3):239-251), ciliates of the types: Holotrichia, Peritrichia, Spirotrichia, Suctoria, Tetrahymena, Paramecium, Colpidium, Glaucoma, Platyophrya, Potomacus, Pseudocohnilembus, Euplotes, Engelmaniella, and Stylonychia, especially of the genus Stylonychia lemnae with vectors following a transformation method as described in PCT Application No. WO 98/01572, and multicellular plant cells (See Schmidt, R. and Willmitzer, L., 1988, High efficiency Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana leaf and cotyledon explants, Plant Cell Rep. 583-586; Plant Molecular Biology and Biotechnology, C Press, Boca Raton, Fla., chapter 6/7, S.71-119 (1993); F. F. White, B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, Eds. Kung And R. Wu, 128-43, Academic Press: 1993; Potrykus, 1991, Annu. Rev. Plant Physiol. Plant Molec. Biol. 42:205-225 and references cited therein) or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press: San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[0140] Expression of polypeptides in prokaryotes is most often carried out with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion polypeptides. Fusion vectors add a number of amino acids to a polypeptide encoded therein, usually to the amino terminus of the recombinant polypeptide but also to the C-terminus or fused within suitable regions in the polypeptides. Such fusion vectors typically serve three purposes: 1) to increase expression of a recombinant polypeptide; 2) to increase the solubility of a recombinant polypeptide; and 3) to aid in the purification of a recombinant polypeptide by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant polypeptide to enable separation of the recombinant polypeptide from the fusion moiety subsequent to purification of the fusion polypeptide. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin, and enterokinase.

[0141] Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S., 1988, Gene 67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase (GST), maltose E binding polypeptide, or polypeptide A, respectively, to the target recombinant polypeptide. In one embodiment, the coding sequence of the PTP is cloned into a pGEX expression vector to create a vector encoding a fusion polypeptide comprising, from the N-terminus to the C-terminus, GST-thrombin cleavage site-X polypeptide. The fusion polypeptide can be purified by affinity chromatography using glutathione-agarose resin. Recombinant PTP unfused to GST can be recovered by cleavage of the fusion polypeptide with thrombin.

[0142] Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., 1988, Gene 69:301-315) and pET 11d (Studier et al, Gene Expression Technology. Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 11d vector relies on transcription from a T7 gn10-lac fusion promoter mediated by a co-expressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident λ prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.

[0143] One strategy to maximize recombinant polypeptide expression is to express the polypeptide in a host bacteria with an impaired capacity to proteolytically cleave the recombinant polypeptide (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128). Another strategy is to alter the sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in the bacterium chosen for expression, such as C. glutamicum (Wada et al, 1992, Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

[0144] In another embodiment, the PTP expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSec1 (Baldari, et al, 1987, EMBO J. 6:229-234), pMFa (Kurjan and Herskowitz, 1982, Cell 30:933-943), pJRY88 (Schultz et al., 1987, Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, Calif.). Vectors and methods for the construction of vectors appropriate for use in other fungi, such as the filamentous fungi, include those detailed in: van den Hondel, C. A. M. J. J. & Punt, P. J., 1991, Gene transfer systems and vector development for filamentous fungi, in: Applied Molecular Genetics of Fungi, J. F. Peberdy, et al., eds., p. 1-28, Cambridge University Press: Cambridge.

[0145] Alternatively, the PTPs of the invention can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of polypeptides in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al, 1983, Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers, 1989, Virology 170:31-39).

[0146] In yet another embodiment, a PTP nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B., 1987, Nature 329:840) and pMT2PC (Kaufman et al., 1987, EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus, and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells, see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

[0147] In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al, 1987, Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton, 1988, Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989, EMBO J. 8:729-733) and immunoglobulins (Banerji et al, 1983, Cell 33:729-740; Queen and Baltimore, 1983, Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989, PNAS 86:5473-5477), pancreas-specific promoters (Edlund et al., 1985, Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example, the murine hox promoters (Kessel and Gruss, 1990, Science 249:374-379) and the fetopolypeptide promoter (Campes and Tilghman, 1989, Genes Dev. 3:537-546).

[0148] For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin, and methotrexate, or in plants that confer resistance towards a herbicide such as glyphosate or glufosinate. Nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector as that encoding a PTP or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid molecule can be identified by, for example, drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).

[0149] In a preferred embodiment of the present invention, the PTPs or the PTE nucleic acid are introduced in plants and plants cells such as unicellular plant cells (e.g. algae) (See Falciatore et al., 1999, Marine Biotechnology 1(3):239-251 and references therein) and plant cells from higher plants (e.g., the spermatophytes, such as crop plants). A PTP or PTE may be “introduced” into a plant cell by any means, including transfection, transformation or transduction, electroporation, particle bombardment, agroinfection, and the like. One transformation method known to those of skill in the art is the dipping of a flowering plant into an Agrobacteria solution, wherein the Agrobacteria contains the PTP or PTE nucleic acid, followed by breeding of the transformed gametes.

[0150] Other suitable methods for transforming or transfecting host cells including plant cells can be found in Sambrook, et al., Molecular Cloning: A Laboratory Manual. 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, and other laboratory manuals such as Methods in Molecular Biology, 1995, Vol. 44, Agrobacterium protocols, Ed: Gartland and Davey, Humana Press, Totowa, N.J. As actively transposing DNA elements are a useful tool, it is desirable that PTPs and/or PTEs be introduced into a wide variety of plants like maize, wheat, rye, oat, triticale, rice, barley, soybean, peanut, cotton, rapeseed and canola, manihot, pepper, sunflower and tagetes, solanaceous plants like potato, tobacco, eggplant, and tomato, Vicia species, pea, alfalfa, bushy plants (coffee, cacao, tea), Salix species, trees (oil palm, coconut), perennial grasses, and forage crops. These crop plants are also preferred target plants for a genetic engineering as one further embodiment of the present invention. Forage crops include, but are not limited to, Wheatgrass, Canarygrass, Bromegrass, Wildrye Grass, Bluegrass, Orchardgrass, Alfalfa, Salfoin, Birdsfoot Trefoil, Alsike Clover, Red Clover, and Sweet Clover.

[0151] In one embodiment of the present invention, transfection of a PTP or PTE into a plant is achieved by Agrobacterium mediated gene transfer. Agrobacterium mediated plant transformation can be performed using for example the GV3101 (pMP90) (Koncz and Schell, 1986, Mol. Gen. Genet. 204:383-396) or LBA4404 (Clontech) Agrobacterium tumefaciens strain. Transformation can be performed by standard transformation and regeneration techniques (Deblaere et al., 1994, Nucl. Acids Res. 13:4777-4788; Gelvin, Stanton B. and Schilperoort, Robert A, Plant Molecular Biology Manual, 2nd Ed.—Dordrecht: Kluwer Academic Publ., 1995.—in Sect., Ringbuc Zentrale Signatur: BT11-P ISBN 0-7923-2731-4; Glick, Bernard R.; Thompson, John E., Methods in Plant Molecular Biology and Biotechnology, Boca Raton: CRC Press, 1993 360 S., ISBN 0-8493-5164-2). For example, rapeseed can be transformed via cotyledon or hypocotyl transformation (Moloney et al., 1989, Plant cell Report 8:238-242; De Block et al., 1989, Plant Physiol. 91:694-701). Use of antibiotics for Agrobacterium and plant selection depends on the binary vector and the Agrobacterium strain used for transformation. Rapeseed selection is normally performed using kanamycin as selectable plant marker. Agrobacterium mediated gene transfer to flax can be performed using, for example, a technique described by Mlynarova et al., 1994, Plant Cell Report 13:282-285. Additionally, transformation of soybean can be performed using for example a technique described in European Patent No. 0424 047, U.S. Pat. No. 5,322,783, European Patent No. 0397 687, U.S. Pat. No. 5,376,543, or U.S. Pat. No. 5,169,770. Transformation of maize can be achieved by particle bombardment, polyethylene glycol mediated DNA uptake or via the silicon carbide fiber technique. (See, for example, Freeling and Walbot “The maize handbook” Springer Verlag: New York (1993) ISBN 3-540-97826-7). A specific example of maize transformation is found in U.S. Pat. No. 5,990,387, and a specific example of wheat transformation can be found in PCT Application No. WO 93/07256.

[0152] According to the present invention, the introduced PTP or PTE nucleic acid may be maintained in the plant cell stably if it is incorporated into a non-chromosomal autonomous replicon or integrated into the plant chromosomes. Alternatively, the introduced PTP or PTE nucleic acid may be present on an extra-chromosomal non-replicating vector and be transiently expressed or transiently active.

[0153] In one embodiment, a homologous recombinant microorganism can be created wherein the PTP is integrated into a chromosome, a vector is prepared which contains at least a portion of a PTP gene into which a deletion, addition, or substitution has been introduced to thereby alter, e.g., functionally disrupt, the PTP gene. Preferably, the PTP gene is a Brassica oleracea, or Oryza sativa PTP gene, but it can be a homolog from a related plant or even from a mammalian, yeast, or insect source. In one embodiment, the vector is designed such that, upon homologous recombination, the endogenous PTP gene is functionally disrupted (i.e., no longer encodes a functional polypeptide; also referred to as a knock-out vector). Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous PTP gene is mutated or otherwise altered but still encodes a functional polypeptide (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous PTP). To create a point mutation via homologous recombination, DNA-RNA hybrids can be used in a technique known as chimeraplasty (Cole-Strauss et al., 1999, Nucleic Acids Research 27(5):1323-1330 and Kmiec, 1999 Gene Therapy American Scientist. 87(3):240-247). Homologous recombination procedures in other organisms are also well known in the art and are contemplated for use herein.

[0154] Whereas in the homologous recombination vector, the altered portion of the PTP gene is flanked at its 5′ and 3′ ends by an additional nucleic acid molecule of the PTP gene to allow for homologous recombination to occur between the exogenous PTP gene carried by the vector and an endogenous PTP gene, in a microorganism or plant. The additional flanking PTP nucleic acid molecule is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several hundreds of base pairs up to kilobases of flanking DNA (both at the 5′ and 3′ ends) are included in the vector. See, e.g., Thomas, K. R., and Capecchi, M. R., 1987, Cell 51:503 for a description of homologous recombination vectors or Strepp et al., 1998, PNAS, 95 (8):4368-4373 for cDNA based recombination in Physcomitrella patens). The vector is introduced into a microorganism or plant cell (e.g., via polyethylene glycol mediated DNA), and cells in which the introduced PTP gene has homologously recombined with an endogenous PTP gene are selected using art-known techniques.

[0155] In another embodiment, recombinant microorganisms can be produced that contain selected systems which allow for regulated expression of the introduced gene. For example, inclusion of a PTP gene on a vector placing it under control of the lac operon permits expression of the PTP gene only in the presence of IPTG. Such regulatory systems are well known in the art.

[0156] Whether present in an extra-chromosomal non-replicating vector or a vector that is integrated into a chromosome, the PTP polynucleotide preferably resides in a plant expression cassette. A plant expression cassette preferably contains regulatory sequences capable of driving gene expression in plant cells that are operatively linked so that each sequence can fulfill its function, for example, termination of transcription by polyadenylation signals. Preferred polyadenylation signals are those originating from Agrobacterium tumefaciens t-DNA such as the gene 3 known as octopine synthase of the Ti-plasmid pTiACH5 (Gielen et al., 1984, EMBO J. 3:835) or functional equivalents thereof but also all other terminators functionally active in plants are suitable. As plant gene expression is very often not limited on transcriptional levels, a plant expression cassette preferably contains other operatively linked sequences like translational enhancers such as the overdrive-sequence containing the 5′-untranslated leader sequence from tobacco mosaic virus enhancing the polypeptide per RNA ratio (Gallie et al., 1987, Nucl. Acids Research 15:8693-8711). Examples of plant expression vectors include those detailed in: Becker, D. et al., 1992, New plant binary vectors with selectable markers located proximal to the left border, Plant Mol. Biol. 20: 1195-1197; and Bevan, M. W., 1984, Binary Agrobacterium vectors for plant transformation, Nuc. Acid. Res. 12:8711-8721; and Vectors for Gene Transfer in Higher Plants; in: Transgenic Plants, Vol. 1, Engineering and Utilization, eds.: Kung and R. Wu, Academic Press, 1993, S. 15-38.

[0157] Gene expression should be operatively linked to an appropriate promoter conferring gene expression in a timely, cell or tissue specific manner. Promoters useful in the expression cassettes of the invention include any promoter that is capable of initiating transcription in a cell.

[0158] The promoter may be constitutive, inducible, developmental stage-preferred, cell type-preferred, tissue-preferred, or organ-preferred. Constitutive promoters are active under most conditions. Examples of constitutive promoters include the CaMV 19S and 35 S promoters (Odell et al., 1985, Nature 313:810-812), the sX CaMV ³⁵S promoter (Kay et al., 1987, Science 236:1299-1302) the Sep1 promoter, the rice actin promoter (McElroy et al., 1990, Plant Cell 2:163-171), the Arabidopsis actin promoter, the ubiquitin promoter (Christensen et al., 1989, Plant Molec Biol 18:675-689); pEmu (Last et al., 1991, Theor Appl Genet 81:581-588), the figwort mosaic virus ³⁵S promoter, the Smas promoter (Velten et al., 1984, EMBO J. 3:2723-2730), the GRP1-8 promoter, the cinnamyl alcohol dehydrogenase promoter (U.S. Pat. No. 5,683,439), promoters from the T-DNA of Agrobacterium, such as mannopine synthase, nopaline synthase, and octopine synthase, the small subunit of ribulose biphosphate carboxylase (ssuRUBISCO) promoter, and the like.

[0159] Inducible promoters are active under certain environmental conditions, such as the presence or absence of a nutrient or metabolite, heat or cold, light, pathogen attack, anaerobic conditions, and the like. For example, the hsp80 promoter from Brassica is induced by heat shock; the PPDK promoter is induced by light; the PR-1 promoter from tobacco, Arabidopsis, and maize are inducible by infection with a pathogen; and the Adhl promoter is induced by hypoxia and cold stress. Plant gene expression can also be facilitated via an inducible promoter (For a review, see Gatz, 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol. 48:89-108). Chemically inducible promoters are especially suitable if gene expression is wanted to occur in a time specific manner. Examples of such promoters are a salicylic acid inducible promoter (PCT Application No. WO 95/19443), a tetracycline inducible promoter (Gatz et al., 1992, Plant J. 2:397-404), and an ethanol inducible promoter (PCT Application No. WO 93/21334).

[0160] In one preferred embodiment of the present invention, the inducible promoter is a stress-inducible promoter. Stress inducible promoters include, but are not limited to, Cor78 (Chak et al., 2000, Planta 210:875-883; Hovath et al., 1993, Plant Physiol. 103:1047-1053), Cor15a (Artus et al., 1996, PNAS 93(23):13404-09), Rci2A (Medina et al., 2001, Plant Physiol. 125:1655-66; Nylander et al., 2001, Plant Mol. Biol. 45:341-52; Navarre and Goffeau, 2000, EMBO J. 19:2515-24; Capel et al., 1997, Plant Physiol. 115:569-76), Rd22 (Xiong et al., 2001, Plant Cell 13:2063-83; Abe et al., 1997, Plant Cell 9:1859-68; Iwasaki et al., 1995, Mol. Gen. Genet. 247:391-8), cDet6 (Lang and Palve, 1992, Plant Mol. Biol. 20:951-62), ADH1 (Hoeren et al., 1998, Genetics 149:479-90), KAT1 (Nakamura et al., 1995, Plant Physiol. 109:371-4), KST1 (Müller-Rober et al., 1995, EMBO 14:2409-16), Rha1 (Terryn et al., 1993, Plant Cell 5:1761-9; Terryn et al., 1992, FEBS Lett. 299(3):287-90), ARSK1 (Atkinson et al., 1997, GenBank Accession # L22302, and PCT Application No. WO 97/20057), PtxA (Plesch et al., GenBank Accession # X67427), SbHRGP3 (Ahn et al., 1996, Plant Cell 8:1477-90), GH3 (Liu et al., 1994, Plant Cell 6:645-57), the pathogen inducible PRP1-gene promoter (Ward et al., 1993, Plant. Mol. Biol. 22:361-366), the heat inducible hsp80-promoter from tomato (U.S. Pat. No. 5,187,267), cold inducible alpha-amylase promoter from potato (PCT Application No. WO 96/12814), or the wound-inducible pinII-promoter (European Patent No. 375091). For other examples of drought, cold, and salt-inducible promoters, such as the RD29A promoter, see Yamaguchi-Shinozalei et al., 1993, Mol. Gen. Genet. 236:331-340. 101601 Developmental stage-preferred promoters are preferentially expressed at certain stages of development. Tissue and organ preferred promoters include those that are preferentially expressed in certain tissues or organs, such as leaves, roots, seeds, or xylem. Examples of tissue preferred and organ preferred promoters include, but are not limited to fruit-preferred, ovule-preferred, male tissue-preferred, seed-preferred, integument-preferred, tuber-preferred, stalk-preferred, pericarp-preferred, and leaf-preferred, stigma-preferred, pollen-preferred, anther-preferred, a petal-preferred, sepal-preferred, pedicel-preferred, silique-preferred, stem-preferred, root-preferred promoters, and the like. Seed preferred promoters are preferentially expressed during seed development and/or germination. For example, seed preferred promoters can be embryo-preferred, endosperm preferred, and seed coat-preferred. See Thompson et al., 1989, BioEssays 10:108. Examples of seed preferred promoters include, but are not limited to, cellulose synthase (celA), Cim1, gamma-zein, globulin-1, maize 19 kD zein (cZ19B1), and the like.

[0161] Other suitable tissue-preferred or organ-preferred promoters include the napin-gene promoter from canola (U.S. Pat. No. 5,608,152), the USP-promoter from Vicia faba (Baeumlein et al, 1991, Mol Gen Genet. 225(3):459-67), the oleosin-promoter from Arabidopsis (PCT Application No. WO 98/45461), the phaseolin-promoter from Phaseolus vulgaris (U.S. Pat. No. 5,504,200), the Bce4-promoter from Brassica (PCT Application No. WO 91/13980), or the legumin B4 promoter (LeB4; Baeumlein et al., 1992, Plant Journal, 2(2):233-9) as well as promoters conferring seed specific expression in monocot plants like maize, barley, wheat, rye, rice, etc. Suitable promoters to note are the lpt2 or lpt1-gene promoter from barley (PCT Application No. WO 95/15389 and PCT Application No. WO 95/23230) or those described in PCT Application No. WO 99/16890 (promoters from the barley hordein-gene, rice glutelin gene, rice oryzin gene, rice prolamin gene, wheat gliadin gene, wheat glutelin gene, oat glutelin gene, Sorghum kasirin-gene, and rye secalin gene).

[0162] Other promoters useful in the expression cassettes of the invention include, but are not limited to, the major chlorophyll a/b binding protein promoter, histone promoters, the Ap3 promoter, the β-conglycin promoter, the napin promoter, the soybean lectin promoter, the maize 15 kD zein promoter, the 22 kD zein promoter, the 27 kD zein promoter, the g-zein promoter, the waxy, shrunken 1, shrunken 2 and bronze promoters, the Zm13 promoter (U.S. Pat. No. 5,086,169), the maize polygalacturonase promoters (PG) (U.S. Pat. Nos. 5,412,085 and 5,545,546), and the SGB6 promoter (U.S. Pat. No. 5,470,359), as well as synthetic or other natural promoters.

[0163] Additional flexibility in controlling heterologous gene expression in plants may be obtained by using DNA binding domains and response elements from heterologous sources (i.e., DNA binding domains from non-plant sources). An example of such a heterologous DNA binding domain is the LexA DNA binding domain (Brent and Ptashne, 1985, Cell 43:729-736).

[0164] The invention further provides a recombinant expression vector comprising a PTP DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner that allows for expression (by transcription of the DNA molecule) of an RNA molecule that is antisense to a PTP mRNA. Regulatory sequences operatively linked to a nucleic acid molecule cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types. For instance, viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific, or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid, or attenuated virus wherein antisense nucleic acids are produced under the control of a high efficiency regulatory region. The activity of the regulatory region can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes, see Weintraub, H. et al., 1986, Antisense RNA as a molecular tool for genetic analysis, Reviews—Trends in Genetics, Vol. 1(1), and Mol et al., 1990, FEBS Letters 268:427-430.

[0165] Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms “host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but they also apply to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein. A host cell can be any prokaryotic or eukaryotic cell. For example, a PTP can be expressed in bacterial cells such as C. glutamicum, insect cells, fungal cells, or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells), algae, ciliates, plant cells, fungi, or other microorganisms like C. glutamicum. Similarly, a PTE nucleic acid can be introduced into any prokaryotic or eukaryotic cell, such as bacterial cells, insect cells, fungal cells, or mammalian cells, algae, ciliates, plant cells, fungi, or other microorganisms. Other suitable host cells are known to those skilled in the art.

[0166] A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) a PTP. Accordingly, the invention further provides methods for producing PTPs using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding a PTP has been introduced, or into which genome has been introduced a gene encoding a wild-type or altered PTP) in a suitable medium until PTP is produced. In another embodiment, the method encompasses the introduction of a heterologous PTE nucleic acid, the production of a PTP from either an endogenous gene or a heterologous gene, resulting in the transposition of the PTE. In another embodiment, the method further comprises isolating PTPs from the medium or the host cell.

[0167] Another aspect of the invention pertains to isolated PTPs, and biologically active portions thereof. An “isolated” or “purified” polypeptide or biologically active portion thereof is free of some of the cellular material when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. The language “substantially free of cellular material” includes preparations of PTP in which the polypeptide is separated from some of the cellular components of the cells in which it is naturally or recombinantly produced. In one embodiment, the language “substantially free of cellular material” includes preparations of a PTP having less than about 30% (by dry weight) of non-PTP material (also referred to herein as a “contaminating polypeptide”), more preferably less than about 20% of non-PTP material, still more preferably less than about 10% of non-PTP material, and most preferably less than about 5% non-PTP material.

[0168] When the PTP or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the polypeptide preparation. The language “substantially free of chemical precursors or other chemicals” includes preparations of PTP in which the polypeptide is separated from chemical precursors or other chemicals that are involved in the synthesis of the polypeptide. In one embodiment, the language “substantially free of chemical precursors or other chemicals” includes preparations of a PTP having less than about 30% (by dry weight) of chemical precursors or non-PTP chemicals, more preferably less than about 20% chemical precursors or non-PTP chemicals, still more preferably less than about 10% chemical precursors or non-PTP chemicals, and most preferably less than about 5% chemical precursors or non-PTP chemicals. In preferred embodiments, isolated polypeptides, or biologically active portions thereof, lack contaminating polypeptides from the same organism from which the PTP is derived. Typically, such polypeptides are produced by recombinant expression of, for example, a Brassica oleracea, or Oryza sativa PTP in plants other than Brassica oleracea, or Oryza sativa, or microorganisms such as C. glutamicum, ciliates, algae or fungi.

[0169] The nucleic acid molecules, polypeptides, polypeptide homologs, fusion polypeptides, primers, vectors, and host cells described herein can be used in one or more of the following methods: identification of Brassica oleracea, or Oryza sativa and related organisms; mapping of genomes of organisms related to Brassica oleracea, or Oryza sativa; identification and localization of Brassica oleracea, or Oryza sativa sequences of interest; evolutionary studies; determination of PTP and PTE regions required for function; modulation of a PTP activity; modulation of the metabolism of one or more cell functions; modulation of the transmembrane transport of one or more compounds; and modulation of expression of PTP nucleic acids.

[0170] The PTP and PTE nucleic acid molecules of the invention have a variety of uses. This invention will be of primary value in the establishment of the first non-transgenic DNA transposable element tagging populations in rice. Such populations will be of value in gene discovery in rice. The mPing/Pong transposable element family will be activated in cell culture and plants regenerated by established procedures. Alternatively, the transposable element family will be activated without using cell culture. Large population of regenerants will be established and mutants identified by visual screening or by biochemical analysis. Mutants will be crossed to wild type plants and the F1 will be selfed. If the F2 population segregates for the mutant phenotype, cells from mutant and wild-type plants will be analyzed by transposon display using the procedures described above to identify mPing or Pong products that co-segregate with the mutant phenotype. These bands will be removed from the gel, reamplified, cloned and sequenced, by established procedures.

[0171] In addition, the nucleic acid and amino acid sequences of the present invention can be used to transform plants, thereby inducing the transposition of a transposable element. The present invention therefore provides a transgenic plant transformed by a PTP or PTE nucleic acid, wherein expression of a PTP in the plant results in increased transposition of a transposable element as compared to a wild type variety of the plant. The transgenic plant can be a monocot or a dicot. The invention further provides that the transgenic plant can be selected from maize, wheat, rye, oat, triticale, rice, barley, soybean, peanut, cotton, rapeseed, canola, manihot, pepper, sunflower, tagetes, solanaceous plants, potato, tobacco, eggplant, tomato, Vicia species, pea, alfalfa, coffee, cacao, tea, Salix species, oil palm, coconut, perennial grass, and forage crops, for example.

[0172] Accordingly, the invention provides a method of producing a transgenic plant with a PTP coding nucleic acid, wherein expression of the nucleic acid in the plant results in increased transposition of a transposable element as compared to a wild type variety of the plant comprising: (a) introducing into a plant cell an expression vector comprising a PTP nucleic acid, and (b) generating from the plant cell a transgenic plant with an increased transposition of a transposable element as compared to a wild type variety of the plant. Also included within the present invention are methods of producing a transgenic plant with a PTE nucleic acid, wherein expression of a PTP in the plant results in increased transposition of the PTE nucleic acid as compared to a wild type variety of the plant comprising: (a) introducing into a plant cell an expression vector comprising a PTE nucleic acid, and (b) generating from the plant cell a transgenic plant with an increased transposition of the PTE nucleic acid as compared to a wild type variety of the plant. The invention further comprises methods of generating a transgenic plant from the transformed plant cell. The plant cell includes, but is not limited to, a protoplast, gamete producing cell, and a cell that regenerates into a whole plant. As used herein, the term “transgenic” refers to any plant, plant cell, callus, plant tissue, or plant part, that contains all or part of at least one recombinant polynucleotide. In many cases, all or part of the recombinant polynucleotide is stably integrated into a chromosome or stable extra-chromosomal element, so that it is passed on to successive generations.

[0173] The invention further provides a method of producing a transgenic plant with a PTP-encoding nucleic acid or a PTE nucleic acid, wherein expression of the nucleic acid in the plant results in increased transposition of a mPing/Pong transposable element as compared to a wild type variety of the plant comprising: (a) transforming a plant cell with an expression vector comprising a PTP-encoding nucleic acid or a PTE nucleic acid, and (b) generating from the plant cell a transgenic plant with an increased tolerance to environmental stress as compared to a wild type variety of the plant. In preferred embodiments, the environmental stress is exposure to herbicides, drought, extreme cold or heat, or salt.

[0174] The present invention also provides a method of modulating the transposition of a transposable element comprising modifying the expression of a PTP coding nucleic acid in the plant. The plant's level of transposition of a transposable element can be increased or decreased as achieved by increasing or decreasing the expression of a PTP, respectively. Preferably, increasing expression of a PTP increases the plant's level of transposition of a transposable element. Expression of a PTP can be modified by any method known to those of skill in the art. The methods of increasing expression of PTPs can be used wherein the plant is either transgenic or not transgenic. In cases when the plant is transgenic, the plant can be transformed with a vector containing any of the above described PTP coding nucleic acids, or the plant can be transformed with a promoter that directs expression of native PTP in the plant, for example. The invention provides that such a promoter can be tissue specific, developmentally regulated, or stress-inducible. Alternatively, non-transgenic plants can have native PTP expression modified by inducing a native promoter. The expression of PTP nucleic acids as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; SEQ ID NO:49 in target plants can be accomplished by, but is not limited to, one of the following examples: (a) constitutive promoter, (b) stress-inducible promoter, (c) chemical-induced promoter, and (d) engineered promoter overexpression with, for example, zinc-finger derived transcription factors (Greisman and Pabo, 1997, Science 275:657).

[0175] In a preferred embodiment, transcription of the PTP is modulated using zinc-finger derived transcription factors (ZFPs) as described in Greisman and Pabo, 1997, Science 275:657 and manufactured by Sangamo Biosciences, Inc. These ZFPs comprise both a DNA recognition domain and a functional domain that causes activation or repression of a target nucleic acid such as a PTP nucleic acid. Therefore, activating and repressing ZFPs can be created that specifically recognize the PTP promoters described above and used to increase or decrease PTP expression in a plant, thereby modulating the levels of transposition of a transposable element of the plant.

[0176] In addition to introducing the PTP and PTE nucleic acid sequences into transgenic plants, these sequences can also be used to identify an organism as being Brassica oleracea, Oryza sativa, or a close relative thereof. Also, they may be used to identify the presence of Brassica oleracea, Oryza sativa, or a relative thereof in a mixed population of microorganisms. The invention provides the nucleic acid sequences of a number of Brassica oleracea, and Oryza sativa genes; by probing the extracted genomic DNA of a culture of a unique or mixed population of microorganisms under stringent conditions with a probe spanning a region of a Brassica oleracea, or Oryza sativa gene which is unique to this organism, one can ascertain whether this organism is present.

[0177] The PTP nucleic acid molecules of the invention are also useful for evolutionary and polypeptide structural studies. By comparing the sequences of the nucleic acid molecules of the present invention to those encoding similar transposase enzymes and transposable elements from other organisms, the evolutionary relatedness of the organisms can be assessed. Similarly, such a comparison permits an assessment of which regions of the sequence are conserved and which are not, which may aid in determining those regions of the polypeptide that are essential for the functioning of the enzyme. This type of determination is of value for polypeptide engineering studies and may give an indication of what the polypeptide can tolerate in terms of mutagenesis without losing function.

[0178] Manipulation of the PTP nucleic acid molecules of the invention may result in the production of PTPs having functional differences from the wild-type PTPs. These polypeptides may be improved in efficiency or activity, may be present in greater numbers in the cell than is usual, or may be decreased in efficiency or activity.

[0179] Additionally, the sequences disclosed herein, or fragments thereof, can be used to generate knockout mutations in the genomes of various organisms, such as bacteria, mammalian cells, yeast cells, and plant cells (Girke, T., 1998, Plant Journal 15:39-48). The resultant knockout cells can then be evaluated for the effect of the transposition on the phenotype and/or genotype of the mutation. For other methods of gene inactivation, see U.S. Pat. No. 6,004,804 “Non-Chimeric Mutational Vectors” and Puttaraju et al., 1999, Nature Biotechnology 17:246252.

[0180] The aforementioned strategies for manipulating PTPs and PTEs resulting in increased transposition of a transposable element are not meant to be limiting; variations on these strategies will be readily apparent to one skilled in the art. Using such strategies, and incorporating the mechanisms disclosed herein, the nucleic acid and polypeptide molecules of the invention may be utilized to generate algae, ciliates, plants, fungi, or other microorganisms like C. glutamicum expressing PTP nucleic acid and polypeptide molecules and containing PTE nucleic acids such that an increase in transposition of a transposable element is observed.

[0181] The present invention also provides antibodies that specifically bind to a PTP, or a portion thereof, as encoded by a nucleic acid described herein. Antibodies can be made by many well-known methods (See, e.g. Harlow and Lane, “Antibodies; A Laboratory Manual,” Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., (1988)). Briefly, purified antigen can be injected into an animal in an amount and in intervals sufficient to elicit an immune response. Antibodies can either be purified directly, or spleen cells can be obtained from the animal. The cells can then fused with an immortal cell line and screened for antibody secretion. The antibodies can be used to screen nucleic acid clone libraries for cells secreting the antigen. Those positive clones can then be sequenced. See, for example, Kelly et al., 1992, Bio/Technology 10:163-167; Bebbington et al., 1992, Bio/Technology 10:169-175.

[0182] The phrases “selectively binds” and “specifically binds” with the polypeptide refer to a binding reaction that is determinative of the presence of the polypeptide in a heterogeneous population of polypeptides and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bound to a particular polypeptide do not bind in a significant amount to other polypeptides present in the sample. Selective binding of an antibody under such conditions may require an antibody that is selected for its specificity for a particular polypeptide. A variety of immunoassay formats may be used to select antibodies that selectively bind with a particular polypeptide. For example, solid-phase ELISA immunoassays are routinely used to select antibodies selectively immunoreactive with a polypeptide. See Harlow and Lane, “Antibodies, A Laboratory Manual,” Cold Spring Harbor Publications, New York, (1988), for a description of immunoassay formats and conditions that could be used to determine selective binding.

[0183] In some instances, it is desirable to prepare monoclonal antibodies from various hosts. A description of techniques for preparing such monoclonal antibodies may be found in Stites et al, Eds., “Basic and Clinical Immunology,” (Lange Medical Publications, Los Altos, Calif., Fourth Edition) and references cited therein, and in Harlow and Lane, “Antibodies, A Laboratory Manual,” Cold Spring Harbor Publications, New York, (1988).

[0184] Throughout this application, various publications are referenced. The disclosures of all of these publications and those references cited within those publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains. The following examples are not intended to limit the scope of the claims to the invention, but are rather intended to be exemplary of certain embodiments. Any variations in the exemplified methods that occur to the skilled artisan are intended to fall within the scope of the present invention.

EXAMPLES Example 1

[0185] Computer Assisted Identification of a New, Potentially Active MITE

[0186] It was reasoned that a potentially active MITE family would have two distinguishing features, (1) low copy number (i.e. it has not amplified significantly) and (2) low intra-family sequence divergence. The availability of almost half of the Nipponbare genome (˜200 Mb) in public databases provided the possibility of identifying such low copy number elements by searching for repeat families with the structural features of MITEs and with very low intra-family sequence divergence. To this end, a two step protocol was employed involving the use of an algorithm to identify repeat families followed by manual screening of the output for a MITE family with virtually identical members. 3200 repeats were identified with RECON (www.genetics.wustl.edu/eddy/recon), a software package for de novo repeat family identification.

[0187] The japonica sequences (187 Mb total) were downloaded from rgp.dna.affrc.gojp on Dec. 24, 2001. The indica sequences (361 Mb total) were downloaded from btn.genomics.org.cn/rice on Feb. 25, 2002. The japonica sequences were used for a systematic identification of repeat families. The sequences were subject to an all-versus-all comparison using WU-BLASTN2.0 (blast.wustl.edu), with options M=5 N=−11 Q=22 R=11−kap E=0.0001−hspmax 5000 wordmask=dust wordmask=seq maskextra=50. The resulting alignments were then clustered into repeat families using RECON (www.genetics.wustl.edu/eddy/recon) with default options. The sequences of the 1257 repeat families obtained with RECON were further examined individually with programs in the University of Wisconsin Genetics Computer Group program suite (GCG, version 10.1) accessed through Research Computing resources (University of Georgia). 3200 total repeats were found. Sequence #1031, termed miniature Ping or mPing (SEQ ID NO:1), was identified as a Tourist-like miniature repeat transposable element (MITE) because (1) its size (430 bp) falls into the range of known MITEs (80-600 bp; (2) its terminal inverted repeat (TIR) is similar to known Tourist elements; (3) its target site duplication (TSD) is TTA or TAA, which is the same for most Tourist MITEs (FIG. 1; Feschotte et al., 2002 Nat Rev Genet., 3(5):329-41).

[0188] The family members of mPing and its related elements in Nipponbare (updated on Feb. 25, 2002) and indica cultivar 93-11 were identified by BLAST search (WU-BLASTN 2.0) using the consensus sequence of mPing (SEQ ID NO:1). From this search, two types of putative autonomous elements were recovered, and named Ping and Pong.

[0189] Of 36 copies of mPing mined from 270 Mb of Nipponbare sequence, 26 were identical while the remaining seven differed at only a single position. A sequence of a consensus mPing element (SEQ ID NO:1) is presented in the Appendix (see FIG. 2 for the GenBank accession numbers). The element has 15 bp TIRs (positions 1-15 and 415-430) and virtually all elements are flanked by the trinucleotide TSD-TAA/TTA. It is estimated that the entire genome should contain 70 copies of mPing. In contrast, only 8 complete copies and 4 half copies of mPing were found in the 361 Mb of publicly available contig sequence of the indica cultivar 93-11 (Table 4). Based on this value, the entire genome of 93-11 is estimated to contain 14 copies of mPing. The 8 complete copies represent two subtypes. Subtype A (SEQ ID NO:1) has 3 members with two identical to the consensus mPing Nipponbare sequence and one differing at a single position. Subtype B (SEQ ID NO:2) has 4 identical members that differ from subtype A by an 11 bp deletion that is centrally located. Subtype C (SEQ ID NO:3) has the same length as subtype A, but the two sequences differ in a centrally located 11 bp region. Subtype D (SEQ ID NO:4) is 450 bp in length. Compared to subtype A, Subtype D has a centrally located 22 bp region that is different from subtype A, and also contains an extra 20 bp in the same region.

Example 2

[0190] Transposition of mPing in Cell Culture

[0191] No DNA transposons had previously been shown to be active in rice. In fact, the only rice transposable elements shown to be active were LTR retrotransposons that transposed in both japonica (Nipponbare) and indica (C5924) cell culture lines (Hirochika, 1993 EMBO J., 12: 2521-2528). Transposition of one of these elements, Tos17, was associated with its transcriptional activation in culture (Hirochika, 1993 EMBO J., 12: 2521-2528). To assess whether mPing elements were also activated in the same cell lines, a technique called transposon display was used to detect new mPing insertions that may have occurred during culturing. Transposon display is a modification of the AFLP procedure that generates PCR products that are anchored in a transposable element and in a flanking restriction site (Casa et al., 2000 Proc. Natl. Acad. Sci. USA, 93: 8524-8529). Since all of the mPing elements are virtually identical at their ends, element-specific primers located in the subterminal sequence were designed to amplify all family members and flanking host sequence.

[0192] Transposon display was performed as described (Casa et al., 2000 Proc. Natl. Acad. Sci. USA, 93: 8524-8529, and in U.S. Pat. No. 6,420,117, herein incorporated by reference in its entirety) with the following modifications. For transposon display with each element, two rounds of PCR (pre-selective amplification and selective amplification) were performed. For each PCR reaction, one of the two nested primers (P1 for pre-selective amplification and P2 for selective amplification, P2 is located downstream of P1) complementary to the subterminal sequence of the element was used. P2 was labeled with ³³P so that the resulting PCR products could be visualized following autoradiography. For selective amplification, a “touchdown” protocol was used where the annealing temperature starts 6° C. higher than the final annealing temperature and is reduced to the final temperature through a 1° C. reduction in temperature per cycle. Adapter sequences are as described.

[0193] For mPing, the primers used for transposon display were P1: TGT GCA TGA CAC ACC AGT G (SEQ ID NO:92); and P2: CAG TGA AAC CCC CAT TGT GAC (SEQ ID NO:93). The temperature cycling parameters used for pre-selective amplification were 72° C. for 2 minutes, 94° C. for 3 minutes, 94° C. for 45 seconds, 58° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, with a final cycle of 72° C. for 5 minutes. The temperature cycling parameters used for selective amplification were 94° C. for 3 minutes, 94° C. for 45 seconds, 64-59° C. for 45 seconds, 72° C. for 45 seconds, touchdown, 94° C. for 45 seconds, 58° C. for 45 seconds, 72° C. 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes.

[0194] Comparison of the number of transposon display products amplified from DNAs isolated from Nippponbare (japonica) and C5924 (indica) plants before culture are consistent with the copy number estimates for mPing family members in the japonica and indica genomes, respectively (FIG. 3). Whereas the Nipponbare band pattern is the same before and after culture, the C5924 culture line has undergone a dramatic increase in the number of PCR products. To determine whether the difference was due to nonspecific genomic rearrangements in this cell line, transposon display was repeated using the same template DNAs but this time, the mPing primer was replaced with either a primer derived from the consensus sequence of two other rice transposable elements. The primer was derived from a gypsy type LTR retrotransposon, SZ-2, or from another rice MITE, ID-1 (Jiang & Wessler, 2001 Plant Cell, 13: 2553-2564).

[0195] For ID-1, the primers used for transposon display were P1: TAT GCT GAC ATG GAT CTC (SEQ ID NO:94), and P2: CTC TTR TAG AGA GCC TAT AG (SEQ ID NO:95). The temperature cycling parameters for pre-selective amplification were 72° C. for 2 minutes, 94° C. for 3 minutes, 94° C. for 45 seconds, 52° C. for 45 seconds, 72° C. 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes. The temperature cycling parameters for selective amplification were 94° C. for 3 minutes, 94° C. for 45 seconds, 61-56° C. for 45 seconds, 72° C. for 45 seconds, touchdown, 94° C. for 45 seconds, 55° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes.

[0196] For SZ-2, the primers used for transposon display were P1: ACG TGG GCG ATT GCG TCT G (SEQ ID NO:96), and P2: TCT GCC TCA AGC CTC TAG TC (SEQ ID NO:97). The temperature cycling parameters for pre-selective amplification were 72° C. for 2 minutes; 94° C. for 3 minutes, 94° C. for 45 seconds, 61° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes. The temperature cycling parameters for selective amplification were 94° C. for 3 minutes; 94° C. for 45 seconds, 66-61° C. for 45 seconds, 72° C. for 45 seconds, touch-down, 94° C. for 45 seconds, 60° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes.

[0197] In contrast to the mPing transposon display, the ID-1 and SZ-2 amplicons were essentially identical before and after cell culture (see FIG. 3).

Example 3

[0198] mPing Targets Low Copy (Genic) Insertion Sites

[0199] In several studies, MITEs have been found predominantly in the noncoding regions of genes (Bureau, et al., 1996 Proc. Natl. Acad. Sci. USA, 93:8524-8529; Zhang, et al., 2000 Proc. Natl. Acad. Sci. USA, 97: 1160-1165; Mao, L. et al., 2000 Genome Res., 10:982-990). They are rarely found in exons or inserted into other classes of repetitive elements. In the absence of actively transposing MITEs, it has not been possible to determine whether this distribution reflects preferential targeting to genic regions or selection against insertion into other regions of the genome. To address this question, 42 amplicons from cell line C5924 were recovered from the transposon display gel, reamplified, subcloned and sequenced.

[0200] The new insertion sites were determined from the transposon display gel. DNA fragments were excised from radioactive gels by scratching the dried gel with yellow tips (Stumm et al., 1997, Elsevier Trends Journals Technical Tips online, http://tto.biomednet.com/cgi-bin/tto/pr) and the tip was placed in 20 μl PCR reaction mix with relevant primers. After a 1 minute incubation, the tips were discarded and the reaction product was reamplified using the same cycling parameters as that of the original reaction. PCR products were resolved in 0.8% agarose gels, fragments were excised, purified (QIAquick, Qiagen, Chatsworth, Calif.) and cloned (TA cloning kit, Invitrogen). DNA templates were sequenced by the Molecular Genetics Instrumentation Facility (University of Georgia). The context of the genomic sequence adjacent to the new insertion was determined using a BLAST search (WU-BLASTN 2.0) of the Nipponbare and 93-11 genomic sequence database. Single copy sequence was defined as a query that results in no more than one hit per genome (except duplicates) with WU-BLASTN 2.0 default parameters.

[0201] The sequences indicate that all products were anchored at one end in an mPing element since the primer sequence was always adjacent to the mPing TIR and TSD sequences. To determine insertion sites of the newly transposed elements, sequences flanking the TIR (37 to 268 bp in length) were used to query the 93-11 and Nipponbare sequences. 34 of 42 flanking sequences matched entries from 93-11 contigs while one of the sequences was only found in japonica (cv. Nipponbare). Thirty-two of the 35 matches were single copy sequences, and one was in a two-copy sequence (see FIG. 2). The remaining two insertion sites were in or were next to other MITEs that were themselves in single copy sequences. Thus, 34 of 35 new insertions were in single copy regions of the genome. Since about 35 to 40% of the available rice genomic sequence is repetitive, these data provide strong evidence that the mPing family targets low copy (genic) regions of the rice genome.

Example 4

[0202] The Amplified Elements

[0203] To isolate the complete transposable element associated with each new insertion event, it was necessary to first determine the sequence flanking the other end of the element (that is, the terminus not represented in the transposon display bands). In ordinary circumstances, this can be a tedious and time-consuming task involving techniques like IPCR or the use of genome walker kits. However, the availability of the indica sequence made this task routine since sequences at the other end of the transposon were adjacent to the flanking sequences recovered from the BLAST searches mentioned above. Host sequences flanking both ends of the transposon were employed in the design of PCR primers that were used with template DNA from the cell line to recover the entire intervening transposon. Virtually all of the new insertions were either the mPingA element (SEQ ID NO:1), or the closely related subtype B (SEQ ID NO:2); subtype C (SEQ ID NO:3), or subtype D (SEQ ID NO:4).

Example 5

[0204] Identification of Candidate Autonomous Elements

[0205] Like other MITE families, mPing elements have no coding capacity and as such, are incapable of catalyzing their own transposition. Thus, movement of mPing must be catalyzed by a transposase encoded in trans. To identify putative autonomous elements, the mPing consensus sequence (SEQ ID NO:1) was used to query all available rice genomic sequence for related, longer elements. A single element with remarkable similarity to mPing was found in the Nipponbare sequence, but was absent from the 93-11 draft sequence. This element, called Ping (SEQ ID NO:5), is 5,341 bp in length and shares 253 bp and 177 bp of its terminal sequence with mPing (See FIG. 1 for comparison to mPing; see FIG. 4 for the GenBank accession number). 429 of 430 bp are identical in the two elements, suggesting that mPing has arisen recently from the larger Pong element by internal deletion.

[0206] Further blast searches using Ping as the query led to the discovery of Pong (SEQ ID NO:8), which is 5,166 bp in length, shares TIRs (the outer 15 bp of its 25 bp TIR are identical to mPing) and similar subterminal regions with mPing and Ping (˜70% over ˜200 bp and ˜40 bp at each end) (See FIG. 1 for comparison). Both Ping and Pong are, like mPing, flanked by 3 bp TSDs of the trinucleotide TAA. While only one copy of Ping was found in Nipponbare (see FIG. 4 for GenBank accession numbers), and there are no copies of Ping in the 93-11 sequence, at least five copies of Pong were found in Nipponbare and six copies of Pong were found in 93-11 (see FIGS. 5 and 6 for the GenBank accession numbers). Eight of ten of the Pong elements appear to be full-length and are almost identical (>99% identity), while two copies were truncated.

Example 6

[0207] Identification of a New Family of Transposases in Plants and Animals

[0208] In addition to their termini, Ping and Pong also share sequence similarity in two blocks of internal sequence corresponding to the two major ORFs of each element (FIG. 1). The predicted size of Ping ORF1 is 172 amino acids (SEQ ID NO:5; positions 2445 to 2663) and 455 amino acids for Pong (SEQ ID NO:8; positions 1630 to 2652), with 80% amino acid identity. ORF2 is predicted to be 455 amino acids for Ping (SEQ ID NO:5; positions 3190 to 4557) and 482 amino acids for Pong (SEQ ID NO:8; positions 2959 to 4407), with 87% amino acid identity. The amino acid sequence of Ping ORF1 is defined in SEQ ID NO:6; the amino acid sequence of Ping ORF2 is defined in SEQ ID NO:7; amino acid sequences of Pong ORF1 are defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; and SEQ ID NO:50; and amino acid sequences of Pong ORF2 are defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; and SEQ ID NO:51.

[0209] When used as queries in tBlastn searches of GenBank, both ORFs yielded numerous hits (E value e⁻¹⁰) from a wide range of plants as well as animals and fungi (FIG. 7). ORF2 homologs are abundant in plants, and most frequently found in organisms with large amounts of genomic sequence in databases: 82 hits (E<e⁻⁴⁶) were from rice, 56 hits (E<e⁻²³) were from Arabidopsis and over 100 hits (E<e⁻³⁶) were from Brassica oleracea. Significantly ORF1 and ORF2 homologs are usually within 2 kb of each other and they are arranged in the same order and orientation as they are in Ping and Pong. Furthermore, several ORF1 and ORF2 pairs are flanked by TIRs and TSDs that are similar to those of Ping and Pong. It is therefore likely that each “pair” of ORF1 and ORF2 homologs belong to the same element.

[0210] The function of ORF1 is unclear. It has only very weak sequence similarity to Myb DNA binding domains (Pfam 7.3, E=0.002). The amino acid sequence of ORF2 revealed little about its identity: although it has numerous homologs in tBlastn searches, they were all unknown or hypothetical proteins. The facts that mPing, Ping and Pong are flanked by 3-bp TTA TSDs and that mPing is a Tourist-like MITE suggested there was a relationship between Ping/Pong and the recently described PIF/IS5 superfamily (Zhang et al., 2001 Proc. Natl. Acad. Sci. USA, 98: 12572-12577). However, the PIF transposase gene was not identified directly in Blast searches as homologous to either of the two ORFs: ORF1 has no homology with PIF transposase, and while ORF2 does have homology to PIF, it does not have the DD47E catalytic motif with the correct spacing as in PIF.

[0211] The first clue to the nature of ORF2 came with the finding that many ORF2 homologs are also related to the PIF transposase. Several such homologs served as “bridges” in a multiple alignment in which they connected ORF2 to the PIF transposase. It is obvious in such an alignment that these homologs fall into two groups: the PIF-like group and the Pong-like group. Significantly, the DD47E motif in PIF aligned with a DD35E motif in ORF2. In addition, the residues surround the DDE motifs that form the N2, N3, and C1 catalytic domains are also very well conserved between PIF transposase and ORF2 (FIG. 3). Moreover, like the PIF transposase, ORF2 is also related to IS5-like elements. While PIF-like elements are more closely related to the ISL2 subgroup, Pong-like elements are closer to the IS1031 subgroup. It was therefore concluded that ORF2 is the transposase gene and that the Pong family is a member of the PIF/IS5 superfamily.

[0212] Although the two ORFs in Ping and Pong are similar and the mPing elements are clearly derived from Ping, several lines of evidence suggest that Ping is not the autonomous element that mobilizes mPing in C5924 cell culture. Ping was only detected as a single copy in Nipponbare: it is absent in the draft sequence of 93-11 (˜84% of the genome) and from 20 of 24 rice cultivars (8 cultivars for each of the following groups: temperate japonica, tropical japonica and indica) tested by PCR, including C5924 itself. Only four temperate japonicas were found to harbor Ping: Nipponbare, Gihobyeo, JX 17 and Koshikari. The apparent absence of Ping from all indica cultivars tested provides strong evidence that it could not be responsible for the movement of mPing elements in the indica cell line. Pong, in contrast, is present in multiple near-identical copies in both indica and japonica. In addition, ORF1 of Ping (SEQ ID NO:6) appears to be truncated at the N terminus compared to its homologs, lacking at least 60 conserved amino acids (FIG. 1). Truncation also extends to a predicted promoter (94%-100% confidence) which is present upstream of ORF1 in Pong (FIG. 1). Finally, compared to the consensus, the Ping ORF2 (SEQ ID NO:7) contains multiple amino acid substitutions especially in conserved catalytic domains, whereas Pong ORF2 (SEQ ID NO:13) has very few substitutions. These data are consistent with a scenario where Ping is a degenerate non-autonomous element that gave rise to mPing MITEs but that the transposase activity resides in one or more of the Pong elements.

Example 7

[0213] Transposition of Pong

[0214] If Pong is the autonomous element responsible for the transposition of mPing elements, it should also be capable of transposition. The fact that there are 8 nearly identical copies of Pong in the Nipponbare and 93-11 sequences suggests that Pong, like the mPing repeat, is still actively transposing. By exploiting the sequence differences between Pong and mPing, PCR primers were designed to amplify Pong elements but not mPing in a transposon display assay. Transposon display was carried out as previously described (Casa et al., 2000 Proc. Natl. Acad. Sci. USA, 93: 8524-8529) with the following modifications.

[0215] For amplification of Pong, the following primers were used: PI: CTT CGT TTC AGC TGA TGT G (SEQ ID NO:98), and P2: ATG TGG CGT CTG GGA AAC AGT G (SEQ ID NO:99). The temperature cycling parameters for pre-selective amplification were 72° C. for 2 minutes, 94° C. for 3 minutes, 94° C. for 45 seconds, 55° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes. The temperature cycling parameters for selective amplification were 94° C. for 3 minutes, 94° C. for 45 seconds, 68-63° C. for 45 seconds, 72° C. for 45 seconds, touch-down, 94° C. for 45 seconds, 62° C. for 45 seconds, 72° C. for 45 seconds for 30 cycles, and a final cycle of 72° C. for 5 minutes.

[0216] As can be seen in FIG. 2, the results with the Pong primers mirror the mPing results. That is, the Pong band number increased dramatically in the indica cell line but remained virtually the same in Nipponbare.

[0217] The nature of the insertion sites and the inserted elements were determined in the same way as was done for mPing.

[0218] Nine out of ten insertion sites were located in single copy sequences (see FIG. 8). Eight newly inserted elements were successfully amplified by PCR and all were indistinguishable in size from Pong.

[0219] The difference in the estimated copy number of mPing elements in a japonica (Nipponbare) and an indica (93-11) genome (70 vs. 14) suggested recent amplification of this MITE family, perhaps since domestication. To assess the timing of amplification, transposon display was undertaken with a panel of O. sativa DNAs to determine the approximate copy number of mPing and Pong elements. As can be seen in FIG. 9A, the temperate japonicas contain the largest number of different mPing-anchored amplicons while the tropical japonicas contain the fewest. This dramatic difference in mPing copy number between the two sub-groups of japonica is significant in light of evidence that the temperate and tropical cultivars are believed to have diverged since domestication (5000-7000 years ago) and are more closely related to each other than either is to indica (Ting, 1957 Acta Agron. Sinica, 8: 243-260; Glaszmann, 1987 Theor. Appl. Genet., 74: 21-30; Wang, et al., 1992 Theor. Appl. Genet., 83: 565-581; Kawakami, et al., 2000 Proc. Natl. Acad. Sci. USA, 97: 11403-11408; Matsuo, et al., 1997 Science of the Rice Plant, Ministry of Agriculture, Forest and Fisheries, Tokyo, Japan; Morishima & Oka, 1981 Japan. J. Breed., 31: 402-413). The different amplicon patterns of Pong elements observed in these cultivars (see FIG. 9B) also suggest that this element has been active since domestication. However, the consistency of amplicon number across cultivars suggests that Pong elements have not significantly increased their copy number.

[0220] It is noted that although Ping appears to be dispensable for the transposition of mPing in the C5924 cell line, the fact that in temperate japonica cultivars the presence of Ping correlated with mPing amplification suggests that Ping may serve as a co-activator (with Pong, perhaps) to enhance transposition of mPing. Furthermore, the requirement for transposition of mPing in plants and in cell culture may be different. The data suggest that one reason for the success of MITEs is an ability to be cross-mobilized by related transposases.

Example 8

[0221] Recent and Explosive Amplification of Pong-Like Elements in Brassica oleracea.

[0222] The transposase of Pong (ORF2, SEQ ID NO:13) was used as query to blast the TIGR Arabidopsis and Brassica oleracea genomic databases. Pong-like transposase is significantly more abundant in Brassica oleracea (139 complete catalytic domains in ˜30% of its genomic sequences) than in its close relative Arabidopsis thaliana (34 in its entire genome). Considering these two species diverged fairly recently (˜10-20 Mya), such a difference may indicate the recent amplification of Pong-like elements in the genome of Brassica oleracea. To explore this possibility, Pong-like transposases in Arabidopsis and Brassica oleracea were compared. A CLUSTALW multiple alignment was constructed from the catalytic domains of 167 Pong-like transposases (139 from Brassica oleracea and 28 from Arabidopsis thaliana) and used to generate a phylogenetic tree (FIGS. 10A and 10B), rooted with the catalytic domain of Pong transposase (ORF2, SEQ ID NO:13).

[0223] Three major lineages were observed in the phylogenetic tree. Two smaller lineages (01 and P2) included sequences from both species and within each lineage no smaller cluster was found to be specific to either species. Therefore, O1 and P2 have clearly diverged prior to the divergence of the Brassicaceae family and neither has significantly amplified in either species. However, a dramatically different picture was observed for the P1 sublineage, which included the majority of the sequences from Arabidopsis and nearly all from Brassica oleracea (137 of 139). Inside P1, Brassica oleracea sequences clustered into four species-specific subgroups (P1b-P1e, P1b not strongly supported), indicating that several lineages of Pong-like elements have undergone recent and explosive amplifications in Brassica oleracea. Interestingly, the amplifications of Pong-like elements appeared to have occurred within a relatively short period of time and followed by a long period of extensive diversification with only sporadic increase in copy number. All sequences from Arabidopsis in P1 also clustered together (P1a). Although such grouping was not strongly supported by Bootstrap values, it suggested that a similar but less dramatic amplification might also have taken place in Arabidopsis.

[0224] In addition to the catalytic domains, over 1,000 Brassica oleracea entries in the TIGR Brassica oleracea database contained homology to various regions of the Pong transposase (ORF2, SEQ ID NO:13). Considering that only ˜30% of the Brassica oleracea genome was available for blast, and that each transposase sequence could have been hit 2-3 times because of the size of each entry in the database (average ˜650 bp), it was roughly estimated that the relatively small genome of Brassica oleracea (˜600 Mb) harbors at least 1,000 Pong-like elements, together contributing as high as 1% of its genome (assuming each element is, like the Pong element, ˜5.0 kb in length). Such a copy number was surprisingly high for plant Class 2 elements and demanded further verification. For this reason homologs of Pong ORF1 in Arabidopsis and Brassica oleracea were also examined. Consistent with the recent amplification of Pong-like elements in Brassica oleracea, ORF1s were found to be significantly more abundant and homologous in its genome (>700 hits in ˜30% genomic sequences, E value <e−10) than in Arabidopsis (21 hits, E value <e−5). In order to compare the phylogeny of ORFIs to that of the transposases, their pairwise association (i.e. a “pair” of ORF 1 and transposase encoded by the same element) was first established. Fourteen of the 21 ORF1 hits from Arabidopsis were located within 2 kb of a transposase and, where element termini were defined, each “pair” was found to belong to the same element. A technical difficulty was encountered for Brassica oleracea. Since its sequences in the GSS database represented the end sequencing (˜650 bp on average) of short genomic clones (˜2.5 kb on average), the association between an ORF1 and a transposase could only be established when they happened to be located on two ends of the same clone, and there was not sufficient sequence information to define element termini. Nevertheless, a significant portion of ORF1 hits (over 200) were found to be associated with transposases, all arranged in the “tail-to-head pattern”. One hundred and eighty five ORF1 hits (6 from Arabidopsis, 179 from Brassica oleracea) contained the entire conserved region, and their evolutionary relationships were determined. The phylogeny of ORF1s was strikingly similar to the phylogeny of their associated transposases. That is, both ORF1s and transposases in Brassica oleracea clustered into four large species-specific subgroups. In addition, based on the pairwise association between ORF1s and transposases, each ORF1 subgroup could be linked to a transposase subgroup, and corresponding subgroups exhibited very similar topology as well as similar numbers of sequences. Taken together, these results confirmed that Pong-like elements have indeed amplified recently and explosively in Brassica oleracea.

Example 9

[0225] Degree of Amino Acid Identity and Similarity of Pong-like ORF1 and ORF2 in Rice and in Brassica

[0226] 13 Pong-like elements in rice (Oryza sativa) were compared at the nucleotide and amino acid level to 188 Pong ORF1-like sequences from Brassica oleracea, and to 140 Pong ORF2-like sequences from Brassica oleracea. The chart below demonstrates the levels of identity and similarity within the rice sequences, within the Brassica sequences, and between rice and Brassica sequences for Pong-like ORF-1 and ORF-2 at the amino acid and nucleotide levels.

[0227] Multiple alignment was performed using the CLUSTALW program available at European Bioinformatics Institute (http://www.ebi.ac.uk/clustalw/) with default parameters (gap opening penalty is 10 and gap extension penalty is 0.05 with blosum62 matrix). Average percentage of sequence similarity was the average of all possible pairwise sequence comparisons. Rice Pong-like ORF1 and ORF2 Average Amino Acid identity in ORFI Full length: 27.76% Conserved region (˜110 a.a.): 37.95% Average Amino Acid Identity in ORF2 Full length: 51.96% Catalytic domain (˜120 a.a.): 65.63% Brassica Pong-like ORFI (˜110 a.a. conserved region) Average Nucleotide Sequences Identity: 59.52% Average Amino Acid Sequences Identity: 65.14% Brassica Pong-like ORF2 (˜120 a.a catalytic domain) Average Nucleotide Sequences Identity: 79.24% Average Amino Acid Sequences Identity: 78.80% Comparison between Rice and Brassica Average Amino Acid Identity in ORF1 (conserved region): 29.03% Average Amino Acid Identity in ORF2 (catalytic domain): 58.22%

Example 10

[0228] Utility In Vivo

[0229] The invention provided herein describes the discovery of the first active DNA transposon system in rice and its activation in cell culture. This invention will be of primary value in the establishment of the first non-transgenic DNA transposable element tagging populations in rice. Such populations should be of value in gene discovery in rice as follows. The mPing/Pong transposable element family will be activated in cell culture and plants regenerated by established procedures. Large population of regenerants will be established and mutants identified by visual screening or by biochemical analysis. Mutants will be crossed to wild type plants and the F1 will be selfed. If the F2 population segregates for the mutant phenotype, cells from mutant and wild-type plants will be analyzed by transposon display using the procedures described above to identify mPing or Pong products that co-segregate with the mutant phenotype. These bands will be removed from the gel, reamplified, cloned and sequenced, by established procedures. 

We claim:
 1. An isolated transposable element comprising at least a portion of a nucleic acid comprising two terminal inverted repeat nucleic acid sequences, wherein the transposable element is actively transposing.
 2. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; and b) a polynucleotide that is complementary to a polynucleotide of a).
 3. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; and b) a polynucleotide that is complementary to a polynucleotide of a).
 4. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:5; and b) a polynucleotide that is complementary to a polynucleotide of a).
 5. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:5; and b) a polynucleotide that is complementary to a polynucleotide of a).
 6. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide having at least 80% sequence identity with a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and b) a polynucleotide that is complementary to a polynucleotide of a).
 7. The transposable element of claim 6, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and b) a polynucleotide that is complementary to a polynucleotide of a).
 8. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:1; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and b) a polynucleotide that is complementary to a polynucleotide of a).
 9. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and b) a polynucleotide that is complementary to a polynucleotide of a).
 10. The transposable element of claim 9, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a nucleic acid encoding a polypeptide having at least 25% sequence identity with a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and b) a polynucleotide that is complementary to a polynucleotide of a).
 11. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and b) a polynucleotide that is complementary to a polynucleotide of a).
 12. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide having at least 50% sequence identity with a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and b) a polynucleotide that is complementary to a polynucleotide of a).
 13. The transposable element of claim 12, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a nucleic acid encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and b) a polynucleotide that is complementary to a polynucleotide of a).
 14. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and b) a polynucleotide that is complementary to a polynucleotide of a).
 15. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide having at least 55% sequence identity with a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and b) a polynucleotide that is complementary to a polynucleotide of a).
 16. The transposable element of claim 15, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and b) a polynucleotide that is complementary to a polynucleotide of a).
 17. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and b) a polynucleotide that is complementary to a polynucleotide of a).
 18. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide having at least 60% sequence identity with a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and b) a polynucleotide that is complementary to a polynucleotide of a).
 19. The transposable element of claim 18, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and b) a polynucleotide that is complementary to a polynucleotide of a).
 20. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and b) a polynucleotide that is complementary to a polynucleotide of a).
 21. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a nucleic acid having at least 75% sequence identity with a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and b) a polynucleotide that is complementary to a polynucleotide of a).
 22. The transposable element of claim 21, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and b) a polynucleotide that is complementary to a polynucleotide of a).
 23. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and b) a polynucleotide that is complementary to a polynucleotide of a).
 24. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a nucleic acid encoding a polypeptide having at least 75% sequence identity with a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and b) a polynucleotide that is complementary to a polynucleotide of a).
 25. The transposable element of claim 24, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and b) a polynucleotide that is complementary to a polynucleotide of a).
 26. The transposable element of claim 1, wherein the transposable element comprises a nucleic acid sequence which hybridizes in 5×SSC at 55° C. to a nucleic acid selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and b) a polynucleotide that is complementary to a polynucleotide of a).
 27. A vector comprising the transposable element of claim
 1. 28. A transgenic eukaryote cell comprising the vector of claim
 27. 29. The transgenic eukaryote cell of claim 28, wherein the cell is a plant cell.
 30. A transgenic plant comprising the plant cell of claim
 29. 31. The plant of claim 30, wherein the plant is a monocot.
 32. The plant of claim 31, wherein the monocot is rice.
 33. The plant of claim 30, wherein the plant is a dicot.
 34. A plant seed produced by the plant of claim
 30. 35. The transgenic eukaryote cell of claim 28, wherein the eukaryote cell is an animal cell.
 36. An isolated nucleic acid probe which selectively hybridizes in 5×SSC at 55° C. to at least a portion of a transposable element comprising two terminal inverted repeat nucleic acid sequences, wherein the transposable element is actively transposing.
 37. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4; and b) a polynucleotide that is complementary to a polynucleotide of a).
 38. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:5; and b) a polynucleotide that is complementary to a polynucleotide of a).
 39. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:8; SEQ ID NO:9; SEQ ID NO:10; SEQ ID NO:11; SEQ ID NO:14; SEQ ID NO:17; SEQ ID NO:20; SEQ ID NO:23; SEQ ID NO:26; SEQ ID NO:29; SEQ ID NO:32; SEQ ID NO:35; SEQ ID NO:38; SEQ ID NO:41; SEQ ID NO:44; SEQ ID NO:47; or SEQ ID NO:49; and b) a polynucleotide that is complementary to a polynucleotide of a).
 40. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:12; SEQ ID NO:15; SEQ ID NO:18; SEQ ID NO:21; SEQ ID NO:24; SEQ ID NO:27; SEQ ID NO:30; SEQ ID NO:33; SEQ ID NO:36; SEQ ID NO:39; SEQ ID NO:42; SEQ ID NO:45; or SEQ ID NO:50; and b) a polynucleotide that is complementary to a polynucleotide of a).
 41. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:13; SEQ ID NO:16; SEQ ID NO:19; SEQ ID NO:22; SEQ ID NO:25; SEQ ID NO:28; SEQ ID NO:31; SEQ ID NO:34; SEQ ID NO:37; SEQ ID NO:40; SEQ ID NO:43; SEQ ID NO:46; SEQ ID NO:48; or SEQ ID NO:51; and b) a polynucleotide that is complementary to a polynucleotide of a).
 42. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:72; SEQ ID NO:74; SEQ ID NO:76; SEQ ID NO:78; SEQ ID NO:80; SEQ ID NO:82; SEQ ID NO:84; SEQ ID NO:86; SEQ ID NO:88; or SEQ ID NO:90; and b) a polynucleotide that is complementary to a polynucleotide of a).
 43. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:73; SEQ ID NO:75; SEQ ID NO:77; SEQ ID NO:79; SEQ ID NO:81; SEQ ID NO:83; SEQ ID NO:85; SEQ ID NO:87; SEQ ID NO:89; or SEQ ID NO:91; and b) a polynucleotide that is complementary to a polynucleotide of a).
 44. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide as defined in SEQ ID NO:52; SEQ ID NO:54; SEQ ID NO:56; SEQ ID NO:58; SEQ ID NO:60; SEQ ID NO:62; SEQ ID NO:64; SEQ ID NO:66; SEQ ID NO:68; or SEQ ID NO:70; and b) a polynucleotide that is complementary to a polynucleotide of a).
 45. The isolated nucleic acid probe of claim 36, wherein the transposable element comprises a nucleic acid sequence selected from the group consisting of: a) a polynucleotide encoding a polypeptide as defined in SEQ ID NO:53; SEQ ID NO:55; SEQ ID NO:57; SEQ ID NO:59; SEQ ID NO:61; SEQ ID NO:63; SEQ ID NO:65; SEQ ID NO:67; SEQ ID NO:69; or SEQ ID NO:71; and b) a polynucleotide that is complementary to a polynucleotide of a). 